Biology subjects

Robertson, G.

Publications and source records attributed to Robertson, G..

At least 19 recordsLinked to original sources

bioRxiv2026

SeqDesk: a sequencing-facility management system for standards-compliant and FAIR (meta)data submission

Achieving FAIR compliance requires both standardized metadata and infrastructure for data deposition, yet in practice a large fraction of sequencing studies is still published without the persistent, standards-compliant metadata that reuse depends on. Collecting MIxS-compliant metadata is complex: environment-specific checklists can contain hundreds of fields, and the effort is magnified when metadata is assembled retrospectively at publication time rather than captured throughout the project. We developed SeqDesk, an open-source data management system for sequencing facilities that is designed so that FAIR-compliant public data is produced as the natural output of routine operations. Its current scope is microbial sequencing data, covering metagenomes as well as isolate genomes, for which it supports the corresponding MIxS checklists. SeqDesk gives a sequencing facility a configurable order-and-tracking system for sequencing projects, captures and validates MIxS-compliant metadata aligned with ENA checklists at project initiation, runs bioinformatics analyses through Nextflow pipelines, and brokers submission to the European Nucleotide Archive, all within the institution's own infrastructure. By embedding standards-compliant metadata capture into the sequencing-facility workflow rather than bolting it on at submission, SeqDesk shortens the path from sample to reusable public data. The underlying checklist model is generic, so support can be extended to further data types and metadata standards beyond the microbial domain. SeqDesk is free and open source under the Apache 2.0 licence and available at https://seqdesk.org, with a live demonstration at https://seqdesk.org/#demo.

bioinformatics↗

bioRxiv2026

An ER retention motif controls the heteromeric stoichiometry of hERG1a/1b channels

The human ether-a-go-go related gene (hERG) encodes a potassium channel essential for cardiac repolarization and neuronal excitability. In the heart, heteromeric assemblies of hERG1a and hERG1b subunits produce cardiac IKr, and mutations in either subunit are associated with long QT syndrome. Although hERG1a and 1b contain identical transmembrane and C-terminal cytosolic domains, they differ in N-terminal cytosolic domains, with hERG1b harboring an arginine-based endoplasmic reticulum (ER) retention/retrieval motif that limits its surface expression in the absence of hERG1a. While the association of hERG1a and 1b subunits is known to influence channel function, the stoichiometry of heteromeric hERG channels and mechanisms that regulate it have remained unresolved. Here, using single molecule photobleaching step analysis in HeLa cells, we show that heteromeric hERG1a/1b channels assemble predominantly with a fixed 2:2 stoichiometry. Mutation of the hERG1b ER retention motif disrupts this bias, resulting in a broader, near-random distribution of subunit compositions. Independent functional assays using dominant-negative pore mutants in Xenopus oocytes yielded quantitative current suppression consistent with a 2:2 assembly and similarly revealed loss of stoichiometric bias upon RXR mutation. Together, these results establish the oligomeric composition of hERG1a/1b channels and identify ER retention as a previously unrecognized determinant of heteromeric stoichiometry. Statement of SignificanceSubunit stoichiometry is a key determinant of ion channel function, yet how defined stoichiometries are established during biogenesis remains poorly understood. Here we demonstrate that heteromeric hERG1a/1b channels assemble with a fixed 2:2 stoichiometry and that an arginine-based ER retention motif in hERG1b is required to maintain this assembly bias. Using single-molecule photobleaching and independent functional assays, we show that disrupting this motif leads to a broadened, near-random distribution of tetrameric subunit compositions. These findings reveal that ER retention contributes not only to quality control and trafficking but also specifies subunit stoichiometry during ion channel assembly.

biophysics↗

bioRxiv2026

Convergent Roles of Growth Differentiation Factor-15 (GDF-15) in Mechanotransduction, Vascular Disorganization, and Immune Suppression in Melanoma

Melanoma, particularly in its advanced forms, remains one of the most lethal skin cancers, with limited effective treatments for both common cutaneous subtypes and rarer variants such as acral melanoma. The effects of the extracellular matrix (ECM) and other cancer-cell extrinsic processes on melanoma development remain underexplored. This study identifies Growth Differentiation Factor-15 (GDF-15) as a novel mechanosensing-regulated driver of melanoma pathogenesis across melanoma types. GDF-15 is shown here to be mechanically induced by ECM rigidity and compressive forces occurring during metastatic progression, leading to significantly elevated levels in both cutaneous and acral melanoma cells. In this study, ECM rigidity was recapitulated using cell-adhesive gelatin methacryloyl (GelMA) hydrogel microparticles (microgels) with tunable stiffness, providing a biomimetic platform to investigate how mechanical cues in the tumor microenvironment regulate GDF-15 expression in melanoma. A previously unrecognized synergy between GDF-15 and inflammatory factors commonly present in tumors was identified and found to promote a disorganized, hyperpermeable vasculature, thereby facilitating tumor nutrient access and impeding effective immune cell infiltration. GDF-15 knockdown reduced the intratumoral hemorrhage phenotype, indicating a causal role. GDF-15 also functions by directly suppressing natural killer (NK) cell-mediated cytotoxicity, revealing a second cooperating mechanism of immune evasion. These effects position GDF-15 as a key node linking mechanical stress, co-operation with inflammatory factors, abnormal vascular development, and immune dysfunction, thereby converging on a pathways and processes not previously described in melanomas. TEASERUncovering GDF-15 as a central mediator at the intersection of mechanical rigidity and external force, disorganized vascular hemorrhagic remodeling, co-operation with inflammatory factors, and immune evasion, revealing a previously unrecognized therapeutic vulnerability across both common and rare melanoma subtypes

cancer biology↗

bioRxiv2025

Comparative Assessment of Large Language Models for Microbial Phenotype Annotation

Large language models (LLMs) are increasingly used to extract knowledge from text, yet their coverage and reliability in biology remain unclear. Microbial phenotypes are especially important to assess, as comprehensive data remain sparse except for well-studied organisms and they underpin our understanding of microbial characteristics, functional roles, and applications. Here, we systematically assessed the biological knowledge encoded in publicly available LLMs for structured phenotype annotation of microbial species. We evaluated the performance of over 50 LLMs, including state-of-the-art models such as Claude Sonnet 4 and the GPT-5 family of models. Across phenotypes, LLMs reached accurate assignments for many species, but performance varied widely by model and trait, and no single model dominated. Model self-reported confidence is informative, with higher confidence aligning with higher accuracy, and can be used to prioritize phenotype assignment, effectively distinguishing between high-and low-confidence inferences. Overall, our study outlines the utility and limitations of text-based LLMs for phenotype characterization in microbiology.

bioinformatics↗

bioRxiv2025

Estimating resource acquisition and water-use traits in wine grapes using reflectance spectroscopy

In agroecosystems, the variable expression of crop functional traits is expected to play a role in key processes, including plant nutrient cycling and water acquisition, that confer ecosystem resistance and/ or resilience to environmental change. The ability to estimate crop trait data is therefore critical to predict crop responses to environmental change, enabling more informed diagnosis of crop performance and on-farm management strategies. Yet, many traditional methods for quantifying plant traits are time-consuming and resource-intensive, limiting sample sizes and study durations. In response, high-throughput phenotyping-- specifically reflectance spectroscopy-- has emerged as a key element of plant trait research, capable of estimating plant traits more rapidly. However, little is known about whether or not reflectance spectroscopy can detect within-species variation in resource acquisition and plant-water traits. Using wine grapes (V. vinifera subsp. vinifera) as a focal crop, this study aimed to assess the ability of reflectance spectroscopy and the subsequent partial least squares regression modelling approach to quantify intraspecific variation in 12 functional traits across 12 different cultivars. Results showed significant differences in traits, especially in the photosynthetic and hydraulic traits, among closely related cultivars, falling along a resource-conservative to resource-acquisitive axis of variation. We also found that reflectance differentiated this fine-scale trait variation, specifically in leaf chemical and morphological traits, contributing to higher accuracy, and indicating that this HTP approach is viable for detailed trait estimation in diverse agroecosystems.

plant biology↗

bioRxiv2025

mRNA interactions promote cotranslational association of heteromeric membrane proteins

Heteromeric membrane proteins play crucial physiological roles, yet how they are formed remains poorly understood. Heteromeric hERG1a/1b ion channels, essential for maintaining normal cardiac rhythm, assemble via cotranslational association of their encoding mRNAs. We hypothesized that direct hERG1a and 1b mRNA interactions facilitate this process. Using fluorescence colocalization and free energy of binding predictions, we found that hERG1a and 1b mRNAs form specific heterotypic condensates in vitro, suggesting direct interactions. When hERG1a mRNA was altered by synonymous mutations predicted to reduce its structural diversity and ability to interact with other mRNAs, overlap with hERG1b was dramatically diminished both in vitro and in cells, indicating weakened interactions. Reducing hERG1a structural diversity also influenced its translational complexes, defined by overlapping between fluorescently labeled mRNA and encoded protein (centroids within 400 nm). Whereas most of the wild-type hERG1a mRNA translates within heterotypic complexes, likely reflecting the biogenesis of hERG1a/1b heteromeric assemblies, reducing hERG1a structural diversity yielded more homotypic translational condensates and fewer hERG1a/1b heterotypic ones. This result suggests that the strength of mRNA interactions impact ion channel biogenesis. Further analysis of the heterotypic translational complexes revealed two distinct classes: a) simultaneous translation of both subunits and b) sequential association of fully translated hERG1b with translating hERG1a. Notably, reducing hERG1a structural diversity and interactions with 1b shifted translation toward the sequential mode. These findings identify a new role of mRNA sequence, structure, and interactions in orchestrating the cotranslational association of important heteromeric membrane proteins. SIGNIFICANCEThe physiological diversity of membrane protein complexes arises in part from the mixing of related yet functionally distinct subunits such as those forming "heteromeric" ion channels. How this mixing is achieved is not well understood. Here, we show that subunits composing heteromeric hERG1a/1b ion channels, crucial for normal cardiac function, predominantly associate in complexes where both subunits are simultaneously translated. This cotranslation is promoted by the association of the encoding mRNAs. Silent mutations disrupting hERG1a and 1b mRNA association, without altering the encoded protein, diminish simultaneous translation in favor of hERG1a translational complexes alone or in association with fully synthesized hERG1b. This study highlights the significant impact of RNA sequence, structure, and association on the formation of heteromeric membrane proteins.

biophysics↗

bioRxiv2025

A mosaic gastruloid model highlights the developmental stage-specific restriction of cell competition in mammalian pre-gastrulation

In early mammalian embryogenesis, the selective elimination of suboptimal cells is critical for developmental integrity. Cell competition (CC) is a cell non-autonomous quality control in which "winner" cells eliminate viable but suboptimal "loser" cells based on their relative difference in fitness. Due to its central role in fitness perception, loss of p53 results in the emergence of "supercompetitor" cells, which stand at the apex of cell competition and induce apoptosis in neighboring wild-type (WT) cells. Here, we investigate CC dynamics using mosaic 3D mouse gastruloids, an embryonic stem cell (ESC)-based in vitro model of gastrulation, composed of defined numbers of WT and p53-KO cells. In mosaic gastruloids, even low numbers of p53-KO cells robustly outcompete WT cells, and introduction of as few as two p53-KO cells is sufficient to measurably impair neighboring WT cell growth. CC in gastruloids is independent of cell proliferation rates, nutrient availability, or reactive oxygen species (ROS), and not influenced by Nodal and ERK signaling. However, we observe that Wnt and BMP signaling protect from CC, which is exclusively driven by intrinsic apoptosis, as indicated by Bcl2-mediated complete rescue of WT cells. During gastruloid development, CC is temporally restricted to a window of 48-96 hours after aggregation, mirroring embryonic days E5.5-E7.5 in the mouse. Heterochronic mosaic gastruloid experiments demonstrate that relative differences in pluripotency levels are neither necessary nor sufficient to cause supercompetition, but that CC is contingent on both competitors residing within the developmental window permissive to CC. Neither pluripotent mosaic 3D aggregates, nor 3D EpiGastruloids, which model more advanced developmental processes, display any competition, supporting the hypothesis that developmental CC is specific to the onset of gastrulation. Our findings offer insights into the mechanisms of cell fitness evaluation in mammalian embryogenesis and establish gastruloids as a powerful 3D model for investigating developmental stage-specific cell competition.

developmental biology↗

bioRxiv2024

Morphogenetic constrains in the development of gastruloids: implications for mouse gastrulation

Mammalian embryonic size is tightly controlled with checkpoints and compensatory mechanisms correcting size defects. Here, we take advantage of gastruloids, a stem cell embryoid system not subject to most size controls, to study the role of size in emergent properties of mammalian embryogenesis. We report that gastruloids exhibit robust morphology and transcriptional profiles within a size range. However, size affects the dynamics, and, outside a range of robust morphogenesis, the precision of anterior-posterior (AP) axial elongation. Gastruloid axial elongation exhibits active cellular contractility, requires planar cell polarity (PCP), adhesion and cell-cell contact remodelling. Smaller gastruloids initiate elongation earlier, correlated with an earlier Brachyury polarisation. Brachyury expression increases tissue fluidity. Axis formation is regulated by the balance of Brachyury multifoci coalescence and the timing of initiation of the elongation programme. Sizes beyond the robust range can modify relative tissue composition. Very small aggregates have increased neural fate bias, accompanied by a loss of paraxial mesoderm mediated by differences in Nodal signalling activity.

developmental biology↗

bioRxiv2024

Phylogenomic reconstruction of Cryptosporidium spp. captured directly from clinical samples reveals extensive genetic diversity

Cryptosporidium is a leading cause of severe diarrhea and mortality in young children and infants in Africa and southern Asia. More than twenty Cryptosporidium species infect humans, of which C. parvum and C. hominis are the major agents causing moderate to severe diarrhea. Relatively few genetic markers are typically applied to genotype and/or diagnose Cryptosporidium. Most infections produce limited oocysts making it difficult to perform whole genome sequencing (WGS) directly from stool samples. Hence, there is an immediate need to apply WGS strategies to 1) develop high-resolution genetic markers to genotype these parasites more precisely, 2) to investigate endemic regions and detect the prevalence of different genotypes, and the role of mixed infections in generating genetic diversity, and 3) to investigate zoonotic transmission and evolution. To understand Cryptosporidium global population genetic structure, we applied Capture Enrichment Sequencing (CES-Seq) using 74,973 RNA-based 120 nucleotide baits that cover [~]92% of the genome of C. parvum. CES-Seq is sensitive and successfully sequenced Cryptosporidium genomic DNA diluted up to 0.005% in human stool DNA. It also resolved mixed strain infections and captured new species of Cryptosporidium directly from clinical/field samples to promote genome-wide phylogenomic analyses and prospective GWAS studies.

genomics↗

bioRxiv2024

Caveolar Compartmentalization is Required for Stable Rhythmicity of Sinus Nodal Cells and is Disrupted in Heart Failure

BackgroundHeart rhythm relies on complex interactions between electrogenic membrane proteins and intracellular Ca2+ signaling in sinoatrial node (SAN) myocytes; however, mechanisms underlying the functional organization of proteins involved in SAN pacemaking and its structural foundation remain elusive. Caveolae are nanoscale, plasma membrane pits that compartmentalize various ion channels and transporters, including those involved in SAN pacemaking, via binding with the caveolin-3 scaffolding protein, but the precise role of caveolae in cardiac pacemaker function is unknown. Our objective was to determine the role of caveolae in SAN pacemaking and dysfunction (SND). MethodsBiochemical co-purification, in vivo electrocardiogram monitoring, ex vivo optical mapping, in vitro confocal Ca2+ imaging, and immunofluorescent and electron microscopy analyses were performed in wild type, cardiac-specific caveolin-3 knockout, and 8-weeks post-myocardial infarction heart failure (HF) mice. SAN tissue samples from donor human hearts were used for biochemical studies. We utilized a novel 3-dimensional single SAN cell mathematical model to determine the functional outcomes of protein nanodomain-specific localization and redistribution in SAN pacemaking. ResultsIn both mouse and human SANs, caveolae compartmentalized HCN4, Cav1.2, Cav1.3, Cav3.1 and NCX1 proteins within discrete pacemaker signalosomes via direct association with caveolin-3. This compartmentalization positioned electrogenic sarcolemmal proteins near the subsarcolemmal sarcoplasmic reticulum (SR) membrane and ensured fast and robust activation of NCX1 by subsarcolemmal local SR Ca2+ release events (LCRs), which diffuse across [~]15-nm subsarcolemmal cleft. Disruption of caveolae led to the development of SND via suppression of pacemaker automaticity through a 50% decrease of the L-type Ca2+ current, a negative shift of the HCN current (If) activation curve, and a 40% reduction of Na+/Ca2+-exchanger function, along with [~]2.3-times widening of the sarcolemma-SR distance. These changes significantly decreased the SAN depolarizing force, both during diastolic depolarization and upstroke phase, leading to bradycardia, sinus pauses, recurrent development of SAN quiescence, and significant increase in heart rate lability. Computational modeling, supported by biochemical studies, identified NCX1 redistribution to extra-caveolar membrane as the primary mechanism of SAN pauses and quiescence due to the impaired ability of NCX1 to be effectively activated by LCRs and trigger action potentials. HF remodeling mirrored caveolae disruption leading to NCX1-LCR uncoupling and SND. ConclusionsSAN pacemaking is driven by complex protein interactions within a nanoscale caveolar pacemaker signalosome. Disruption of caveolae leads to SND, potentially demonstrating a new dimension of SAN remodeling and providing a newly recognized target for therapy.

physiology↗

bioRxiv2024

In silico genomic surveillance by CoVerage predicts and characterizes SARS-CoV-2 Variants of Interest

Rapidly evolving viral pathogens such as SARS-CoV-2 continuously accumulate amino acid changes, some of which affect transmissibility, virulence or improve the virus ability to escape host immunity. Since the beginning of the pandemic and establishment of SARS-CoV-2 as a human pathogen, multiple lineages with concerning phenotypic alterations, so called Variants of Concern (VOCs), have emerged and risen to predominance. To optimize public health management and to ensure the continued efficacy of vaccines, the early detection of such variants of interest is essential. Therefore, large-scale viral genomic surveillance programs have been initiated worldwide, with data being deposited in public repositories in a timely manner. However, technologies for their continuous interpretation are currently lacking. Here, we describe the CoVerage system (www.sarscoverage.org) for viral genomic surveillance, which continuously predicts and characterizes novel and emerging potential Variants of Interest (pVOIs) from country-wise lineage frequency dynamics together with their antigenic and evolutionary alterations utilizing the GISAID viral genome resource. In a comprehensive assessment of VOIs, VOCs and VUMs identified, we demonstrate how CoVerage can be used to swiftly identify and characterize such variants, with a lead time of almost three months relative to them reaching their maximal abundances. CoVerage can facilitate the timely identification and assessment of future SARS-CoV-2 variants relevant for public health.

bioinformatics↗

bioRxiv2023

High throughput screening of Leaf Economics traits in six wine grape varieties

Reflectance spectroscopy has become a powerful tool for non-destructive and high- throughput phenotyping in crops. Emerging evidence indicates that this technique allows for estimation of multiple leaf traits across large numbers of samples, while alleviating the constraints associated with traditional field- or lab-based approaches. While the ability of reflectance spectroscopy to predict leaf traits across species and ecosystems has received considerable attention, whether or not this technique can be applied to quantify within species trait variation have not been extensively explored. Employing reflectance spectroscopy to quantify intraspecific variation in functional traits is especially appealing in the field of agroecology, where it may present an approach for better understanding crop performance, fitness, and trait-based responses to managed and unmanaged environmental conditions. We tested if reflectance spectroscopy coupled with Partial Least Square Regression (PLSR) predicts rates of photosynthetic carbon assimilation (Amax), Rubisco carboxylation (Vcmax), electron transport (Jmax), leaf mass per area (LMA), and leaf nitrogen (N), across six wine grape (Vitis vinifera) varieties (Cabernet Franc, Cabernet Sauvignon, Merlot, Pinot Noir, Viognier, Sauvignon Blanc). Our PLSR models showed strong capability in predicting intraspecific trait variation, explaining 55%, 58%, 62%, and 64% of the variation in observed Jmax, Vcmax, leaf N, and LMA values, respectively. However, predictions of Amax were less strong, with reflectance spectra explaining only 29% of the variation in this trait. Our results indicate that trait variation within species and crops is less well-predicted by reflectance spectroscopy, than trait variation that exists among species. However, our results indicate that reflectance spectroscopy still presents a viable technique for quantifying trait variation and plant responses to environmental change in agroecosystems.

ecology↗

bioRxiv2023

Age-induced midbrain-striatum assembloids model early phenotypes of Parkinsons disease

Parkinsons disease (PD), one of the most common aging-associated neurodegenerative disorders, is characterised by nigrostriatal pathway dysfunction, caused by the gradual loss of dopaminergic neurons in the substantia nigra pars compacta (SNpc) of the midbrain and the dopamine depletion in the striatum. State of the art, human in vitro models are enabling the study of the dopaminergic neurons loss, but not the dysregulation of the dopaminergic network in the nigrostriatal pathway. Additionally, these models do not incorporate aging characteristics which potentially contribute to the development of PD. Therefore, it is conceivable that research conducted using these models overlooked numerous processes that contribute to diseases phenotypes. Here we present a nigrostriatal pathway model based on midbrain-striatum assembloids with inducible aging. We show that these assembloids are capable of developing characteristics of the nigrostriatal connectivity, with catecholamine release from the midbrain to striatum and synapse formation between midbrain and striatal neurons. Moreover, Progerin-overexpressing assembloids acquire aging traits that lead to early phenotypes of PD. This new model shall help to reveal the contribution of aging as well as nigrostriatal connectivity to the onset and progression of PD.

neuroscience↗

bioRxiv2023

An intracellular hydrophobic nexus is critical for slow deactivation in hERG channels

Slow deactivation is a critical biophysical and physiological property of voltage-gated K+ channels encoded by the human Ether-a-go-go-Related Gene (hERG). hERG channel deactivation is modulated by interactions between intracellular N-terminal Per-Arnt-Sim (PAS) and C-terminal cyclic nucleotide-binding homology (CNBh) domains. The PAS domain is multipartite, comprising a globular domain (residues 26-136) and an N-terminal PAS-cap that is further subdivided into an initial unstructured segment (residues 1-12) and an amphipathic -helical region (residues 13-25). Disruption of interactions within the PAS-CNBhD complex accelerates deactivation kinetics and impairs the slow repolarization of the cardiac action potential. Similarly, deletion of the PAS-cap unstructured segment, modeled as a "foot-in-the-door," accelerates channel closing. Here, we tested the hypothesis that a three-dimensional hydrophobic nexus, comprising residues in the PAS-cap -helix, the globular PAS, and CNBh domains, plays a crucial role in slow deactivation. Utilizing structure-directed mutagenesis, electrophysiology, and molecular dynamics simulations, we provide evidence that altering hydrophobicity at this interface accelerates deactivation kinetics and causes a rearrangement in the network of residues comprising the hydrophobic nexus. Moreover, the PAS-cap unstructured segment disengages from the gating machinery. We propose that the nexus hydrophobicity positions the PAS-cap -helix and promotes engagement of the upstream PAS-cap unstructured segment with the gating machinery, resulting in slow channel closing. Interestingly, several long QT syndrome disease mutations lie at this interface, underscoring the importance of the hydrophobic nexus and the novel role of the PAS-cap -helix in hERG gating.

biophysics↗

bioRxiv2022

Microglia integration into human midbrain organoids leads to increased neuronal maturation and functionality.

The human brain is a complex, three-dimensional structure. To better recapitulate brain complexity, recent efforts have focused on the development of human specific midbrain organoids. Human iPSC-derived midbrain organoids consist of differentiated and functional neurons, which contain active synapses, as well as astrocytes and oligodendrocytes. However, the absence of microglia, with their ability to remodel neuronal networks and phagocytose apoptotic cells and debris, represents a major disadvantage for the current midbrain organoid systems. Additionally, neuro-inflammation related disease modeling is not possible in the absence of microglia. So far, no studies about the effects of human iPSC-derived microglia on midbrain organoid neural cells have been published. Here we describe an approach to derive microglia from human iPSCs and integrate them into iPSC-derived midbrain organoids. Using single nuclear RNA Sequencing, we provide a detailed characterization of microglia in midbrain organoids as well as the influence of their presence on the other cells of the organoids. Furthermore, we describe the effects that microglia have on cell death and oxidative stress- related gene expression. Finally, we show that microglia in midbrain organoids affect synaptic remodeling and increase neuronal excitability. Altogether, we show a more suitable system to further investigate brain development, as well as neurodegenerative diseases and neuro- inflammation. Main Points- Macrophage precursors can be efficiently co-cultured with midbrain organoids, they integrate into the tissue and differentiate into microglia in 3D. - Organoids containing microglia have a smaller size and show a down-regulation of oxidative stress-related genes. - Organoids co-cultured with microglia show differences in genes related to synaptic remodeling and action potential, as well as a more spontaneous action potential firing.

neuroscience↗

bioRxiv2022

Transatlantic spread of highly pathogenic avian influenza H5N1 by wild birds from Europe to North America in 2021

Highly pathogenic avian influenza (HPAI) viruses of the A/Goose/Guangdong/1/1996 lineage (GsGd), which threaten the health of poultry, wildlife and humans, are spreading across Asia, Europe and Africa, but are currently absent from Oceania and the Americas. In December 2021, H5N1 HPAI viruses were detected in poultry and a free-living gull in St. Johns, Newfoundland and Labrador, Canada. Phylogenetic analysis showed that these viruses were most closely related to HPAI GsGd viruses circulating in northwestern Europe in spring 2021. Analysis of wild bird migration suggested that these viruses may have been carried across the Atlantic via Iceland, Greenland/Arctic or pelagic routes. The here documented incursion of HPAI GsGd viruses into North America raises concern for further virus spread across the Americas by wild bird migration. One-Sentence SummaryDetection of H5N1 highly pathogenic avian influenza in Canada raises concern for spread in the Americas by migratory birds.

microbiology↗

bioRxiv2021

Critical Assessment of Metagenome Interpretation - the second round of challenges

Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the community-driven initiative for the Critical Assessment of Metagenome Interpretation (CAMI). In its second challenge, CAMI engaged the community to assess their methods on realistic and complex metagenomic datasets with long and short reads, created from [~]1,700 novel and known microbial genomes, as well as [~]600 novel plasmids and viruses. Altogether 5,002 results by 76 program versions were analyzed, representing a 22x increase in results. Substantial improvements were seen in metagenome assembly, some due to using long-read data. The presence of related strains still was challenging for assembly and genome binning, as was assembly quality for the latter. Taxon profilers demonstrated a marked maturation, with taxon profilers and binners excelling at higher bacterial taxonomic ranks, but underperforming for viruses and archaea. Assessment of clinical pathogen detection techniques revealed a need to improve reproducibility. Analysis of program runtimes and memory usage identified highly efficient programs, including some top performers with other metrics. The CAMI II results identify current challenges, but also guide researchers in selecting methods for specific analyses.

bioinformatics↗

bioRxiv2020

Burkholderia pseudomallei clinical isolates are highly susceptible in vitro to cefiderocol, a novel siderophore cephalosporin

Cefiderocol is a novel cephalosporin designed to treat multidrug resistant Gram-negative infections. By forming a chelated complex with ferric iron, cefiderocol is transported into the periplasmic space via bacterial iron transport systems and primarily binds to penicillin-binding protein 3 (PBP3) to inhibit peptidoglycan synthesis. This mode of action results in cefiderocol having greater in vitro activity against many Gram-negative bacilli than currently used carbapenems, {beta}-lactam/{beta}-lactamase inhibitor combinations, and cephalosporins. Thus, we investigated the in vitro activity of cefiderocol (S-649266) against a total of 271 clinical isolates of Burkholderia pseudomallei from Australia. The collection was comprised of primary isolates (92.3%) and subsequent isolates (7.7%). Minimum inhibitory concentrations (MIC) of cefiderocol ranged from [≤]0.03 to 32 mg/L, where the MIC90 was 1 mg/L and 16 mg/L for primary and subsequent isolates, respectively. Based upon non-species specific (Gram-negative bacilli) clinical breakpoints for cefiderocol (MIC [≤] 4 mg/L), twelve isolates (4.4%) would be classified as non-susceptible. Further testing for co-resistance to meropenem, ceftazidime, trimethoprim-sulfamethoxazole, amoxicillin-clavulanate and doxycycline was performed on a subset of isolates with elevated cefiderocol MICs ([≥]2 mg/L, 4.8%) and 84.6% of these isolates exhibited resistance to at least one of these antimicrobials. Cefiderocol was found to be highly active in vitro against B. pseudomallei primary clinical isolates. This novel compound shows great potential for the treatment of melioidosis in endemic countries and should be explored further.

microbiology↗