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Vos, M.

Publications and source records attributed to Vos, M..

At least 19 recordsLinked to original sources

Projected habitat loss and spatial redistribution of two alpine and subalpine species in Himachal Pradesh, Western Himalaya under CMIP6 scenarios

Climate change will alter habitat suitability for plant communities in mountain ecosystems of the Western Himalaya. There will be contrasting magnitudes and spatial configurations of these changes for different plant species, and it is an important question how to translate these contrasts into effective climate-proof multi-species conservation planning. This study assessed current habitat associations and projected changes in suitable habitat for two contrasting species, Meconopsis aculeata and Rhododendron campanulatum, in Himachal Pradesh, India. Field surveys and spatially filtered occurrence records were combined with MaxEnt modelling using 10 non-collinear environmental predictors. Habitat suitability was projected to 2050 and 2070 under Shared Socioeconomic Pathways; SSP1-2.6, SSP2-4.5 and SSP5-8.5 using HadGEM3-GC31-LL. Field observations showed contrasting habitat associations, with M. aculeata occurring mainly in open alpine herbaceous communities and R. campanulatum in subalpine woody communities. Elevation was an important predictor for both species while climatic predictors contributed differently to their relative importance and response patterns. Future projections indicated reductions in suitable habitat of approximately 25% for M. aculeata and 27-28% for R. campanulatum. Habitat-change maps showed heterogeneous patterns of loss, gain and persistence rather than uniform contraction, and centroid displacement remained small (7.7-8.5 km). We performed proximity analyses to show which currently suitable areas are most close to areas of future gain, in order to support the design of climate-proof protected areas. We discuss how interspecific differences in response are relevant to multi-species conservation planning that considers the spatial relationship between current high-suitability areas and the gain, loss and redistribution of future suitable habitat.

ecology↗

Structural determinants of endopilus assembly, stability and functional specificity in bacterial type II secretion

Gram-negative bacteria employ the type II secretion system (T2SS) to transport folded protein effectors across the outer membrane. This multiprotein nanomachine assembles the endopilus, a periplasmic helical polymer composed of one major and four minor pilin subunits. Endopili are structurally related to type IV pili but exhibit distinct features including a conserved calcium-binding site stabilizing their major pilin subunits. Endopilus polymerisation is coupled to substrate translocation through a dedicated outer membrane channel. To investigate the structural basis of endopilus assembly, stability and functional specificity, we performed a comparative analysis of the Out T2SS from the plant pathogen Dickeya dadantii and the Pul T2SS from the human pathogen Klebsiella oxytoca. Although their major pilins OutG and PulG share over 77% sequence identity, these bacteria differ markedly in ecological niche and range of secreted effectors. We report here the NMR structure of calcium-bound OutG monomer and cryo-EM structures of OutG and PulG endopili at 3.6 [A] resolution. The integration of structural, mutational, and biophysical analyses with in vivo assays, allowed us to identify the molecular determinants of secretion specificity and endopilus stability. These findings demonstrate how subtle sequence variations in conserved nanomachines have evolved to optimize their function and adapt to their local environments.

microbiology↗

Uncompromised, multimodal, multiscale structural analysis of the hierarchically organization in mineralized tissues

We present a live-to-cryo correlative imaging workflow for multiscale structural and chemical analysis of biological tissues in their near-native state. The method integrates live super-resolution fluorescence microscopy, live and cryogenic Raman spectroscopy, and targeted cryogenic focused ion beam/scanning electron microscopy, transmission electron microscopy, electron tomography, energy dispersive X-ray spectroscopy, and electron diffraction. This approach enables precise 3D targeting and nanoscale imaging of selected regions across four orders of magnitude in spatial resolution, while preserving ultrastructure and chemical composition. Using regenerating zebrafish scales as a benchmark, we visualize collagen fibril orientation, local matrix density, and mineral composition within the extracellular matrix. We identify a plywood-like architecture of unmineralized collagen with orientation-independent density variation, and reveal curved, acidic phosphate-rich mineral platelets aligned with collagen fibrils. This workflow establishes a generalizable strategy for comprehensive 3D correlative analysis of hybrid tissues, and opens new opportunities for studying native structure-function relationships at the interface of biology and materials science.

biophysics↗

A simple test demonstrates that many prokaryotic accessory genes are adaptive.

Bacterial genomes often contain many genes that are only present in a subset of strains, the so-called accessory genes. Whether these genes are adaptive, neutral or deleterious remains contentious. Here we introduce a simple test to differentiate between these possibilities. If an accessory gene is adaptive then the sequence of the gene should be conserved, and the ratio of non-synonymous to synonymous diversity,{pi} n/{pi}s, should be less than one. In contrast, if the gene is neutral or deleterious, selection should not conserve the gene sequence, and{pi} n/{pi}s should equal one. We apply this test to accessory genes in Escherichia coli and Staphylococcus aureus, two highly divergent bacterial species with a large and a small pangenome respectively. We find{pi} n/{pi}s<1 for genes at all frequencies in both species demonstrating that many are adaptive. We estimate that at least 75% of all the accessory genes are maintained by selection in the two species that we have analysed, equating to thousands of adaptive accessory genes in both species, a substantial increase on previous estimates. Significance statementMany bacterial genes are found in only a subset of the strains of a bacterial species. These are referred to as accessory genes. Whether, accessory genes are adaptive, allowing certain strains to inhabit particular niches, remains a highly contentious question. In this paper we introduce a simple test of whether accessory genes are adaptive and show that >75% of them are, in two highly divergent bacterial species. This radically alters our view of this type of genetic variation and bacterial evolution.

evolutionary biology↗

Nitrate-responsive Mycobacterial Intracytoplasmic Membranes dampen Inflammation during Mycobacterium tuberculosis Infection

Subcellular compartmentalization of metabolic processes is a main feature of prokaryotic and eukaryotic architecture. Environmental bacteria generate intracytoplasmic membranes (ICMs) as a crucial strategy to adapt their metabolism to environmental changes. While pathogenic intracellular bacteria also perceive various stressful stimuli during host interactions, the subsequent re-organization of their internal architecture has not been explored. Using cryo-electron tomography, we show that Mycobacterium tuberculosis (Mtb), a major human pathogen, is able to form ICMs outside and inside host cells in a strain-dependent manner. We characterize these Mycobacterial intracytoplasmic Membranes (MIMs) as nitrate-induced structures involved in regulation of metabolism. Furthermore, we uncover that MIM formation during macrophage infection correlates with the ability of Mtb to dampen cellular inflammatory responses. Our findings reveal a previously uncharacterized cytoplasmic structure in Mtb and link it to a functional mechanism that enables the bacterium to adapt to its intracellular niche.

microbiology↗

Bridging the resolution gap in cryo-CLEM by introducing cryo-SXT: cryo-CLXEM

Cryo-imaging in cellular biology provides the means to visualize the cellular interieur at close-to-native conditions. A cornerstone in the field has been cryo-correlative light and electron microscopy (cryo-CLEM), with cryo-visible light fluorescent microscopy (cryo-VLFM) providing the specificity by tagging macromolecules or structures and cryo-electron tomography (cryo-ET) for the structural details at molecular level. The large resolution gap between these techniques, however, is limiting this correlative workflow as cryo-ET targets are often smaller than the resolution limit of cryo-VLFM. Here we introduce cryo-soft X-ray tomography (cryo-SXT) as an intermediate step that can compensate for the partial view and limited resolution of cryo-VLFM by providing invaluable cellular context information in 3D to the cryo-ET dataset within an integrated workflow.

cell biology↗

Large Language Model-assisted text mining reveals bacterial pathogen diversity

Compiling and characterising the diversity of bacterial pathogens of humans is a critical challenge to tackle infection risk, especially in the context of global antimicrobial resistance, climate change, and changing demographics. Here, we present a scalable, automated pipeline that harnesses large language models (LLMs) to systematically mine the biomedical literature for information of human pathogenicity across the bacterial domain. By interrogating tens of thousands of PubMed abstracts we identify 1,222 species with at least one abstract documenting human infection, of which 783 species are supported by 3 or more abstracts and are regarded as "confirmed pathogens". We extract, summarise, visualise and interpret data on infection contexts using both expert-curated LLM prompts and unsupervised text vectorisation. We show that these methods enable fine-grained trait mapping across taxa, including quantifying the degree of specialism or generalism in body site specificity for different taxa and the classification of pathogen species into 75 "pathogen types". An objective measure of the rate at which species are reported in the literature coupled to species clustering offers insights into the drivers of pathogen emergence. Our LLM-driven strategy generates an open, updatable, evidence-based catalogue of bacterial human pathogens and their ecological and clinical traits, providing a foundation for public health surveillance, diagnostics, and predictive modelling. This work demonstrates the potential of AI-assisted literature synthesis to transform our understanding of microbial diversity, including its impact on human health.

microbiology↗

TYPE THREE SECRETION SYSTEM-INDUCED MECHANOPORATION OF VACUOLAR MEMBRANES

SO_SCPLOWUMMARYC_SCPLOWEndomembrane breaching is a crucial strategy employed by intracellular pathogens enclosed within vacuoles to access the nutrient-rich cytosol for intracellular replication. While bacteria use various mechanisms to compromise host membranes, the specific processes and factors involved are often unknown. Shigella flexneri, a major human pathogen, accesses the cytosol relying on the Type Three Secretion System (T3SS) and secreted effectors. Using in-cell correlative light and electron microscopy, we tracked the sequential steps of Shigella host cell entry. Moreover, we captured the T3SS, which projects a needle from the bacterial surface, in the process of puncturing holes in the vacuolar membrane. This initial puncture ensures disruption of the vacuolar membrane. Together this introduces the concept of mechanoporation via a bacterial secretion system as a crucial process for bacterial pathogen-induced membrane damage. GO_SCPLOWRAPHICALC_SCPLOW AO_SCPLOWBSTRACTC_SCPLOW O_FIG O_LINKSMALLFIG WIDTH=199 HEIGHT=200 SRC="FIGDIR/small/613840v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@1669028org.highwire.dtl.DTLVardef@8259cborg.highwire.dtl.DTLVardef@1d522caorg.highwire.dtl.DTLVardef@1df0f2d_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

Legacy effects of extreme events

Global change is increasing the intensity of environmental extremes. Abiotic extremes include hotter summers and more intense heatwaves1-2. Biotic extremes include disproportionate increases in herbivory3. Both have well-understood immediate impacts on the plant communities that support life across the globe. However, their longterm effects are difficult to predict, as it is unknown how heat and herbivory differ in the way they create historical legacies. These are changes in a community that still affect dynamics and recovery long after a disturbance has passed. Here we show differences in legacy construction by mild and extreme heatwaves and small- and large-bodied herbivores. We analysed patterns in the population dynamics of a consumer added to replicated primary producer communities after disturbance had ended. We find that the legacy induced by extreme heat drives post-disturbance consumer declines in all replicates. This results in stochastic extinctions as the loss of populations becomes more likely when their density gets close to zero. In contrast, the legacy created by the large-bodied herbivore does not drive extinctions. It diminishes population growth by orders of magnitude across six generations. The observed effects appear after a time-lag that is shorter for extreme heat than for herbivory. Our results show that legacy effects drive complex causal sequences that may involve deterministic and chance components, time-lags, stressor amplification and regime shifts. Insight in how these combine to shape the future is essential for our capacity to accurately forecast and repair the consequences of global change.

ecology↗

Putting the Asymmetric Response Concept to the test: modeling multiple stressor exposure and release in a stream food web

Communities in stream ecosystems often respond asymmetrically to increase and release of stressors, as indicated by slow and incomplete recovery. The Asymmetric Response Concept (ARC) posits that this is due to a shift in the relative importance of three mechanisms: tolerance, dispersal, and biotic interactions. In complex natural communities, these mechanisms may produce alternative outcomes through poorly understood indirect effects. To understand how the three mechanisms respond to different temporal stressor scenarios, we studied multiple scenarios using a stream food web model. We asked the following questions: Do groups of species decline as expected on the basis of individual tolerance rankings derived from laboratory experiments when they are embedded in a complex dynamic food web? Does the response of ecosystem function match that of communities? To address these questions, we aggregated data on individual tolerances at the level of functional groups and studied how single and multiple stressors affect food web dynamics and nutrient cycling. Multiple stressor scenarios involved different intensities of salt and temperature increase. Functional groups exhibited a different relative tolerance ranking between the laboratory and dynamic food web contexts. Salt as a single stressor had only minor and transient effects at low level but led to the loss of one or more functional groups at high level. In contrast, high temperature, alone or in combination with salt, caused the loss of functional groups at all tested levels. Patterns often differed between the response of communities and ecosystem function. We discuss our findings with respect to the ARC. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/601677v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@2924f0org.highwire.dtl.DTLVardef@138400aorg.highwire.dtl.DTLVardef@1f45126org.highwire.dtl.DTLVardef@fba006_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

NRF2-dependent regulation of the prostacyclin receptor PTGIR drives CD8 T cell exhaustion

The progressive decline of CD8 T cell effector function--also known as terminal exhaustion--is a major contributor to immune evasion in cancer. Yet, the molecular mechanisms that drive CD8 T cell dysfunction remain poorly understood. Here, we report that the Kelch-like ECH-associated protein 1 (KEAP1)-Nuclear factor erythroid 2-related factor 2 (NRF2) signaling axis, which mediates cellular adaptations to oxidative stress, directly regulates CD8 T cell exhaustion. Transcriptional profiling of dysfunctional CD8 T cells from chronic infection and cancer reveals enrichment of NRF2 activity in terminally exhausted (Texterm) CD8 T cells. Increasing NRF2 activity in CD8 T cells (via conditional deletion of KEAP1) promotes increased glutathione production and antioxidant defense yet accelerates the development of terminally exhausted (PD-1+TIM-3+) CD8 T cells in response to chronic infection or tumor challenge. Mechanistically, we identify PTGIR, a receptor for the circulating eicosanoid prostacyclin, as an NRF2-regulated protein that promotes CD8 T cell dysfunction. Silencing PTGIR expression restores the anti-tumor function of KEAP1-deficient T cells. Moreover, lowering PTGIR expression in CD8 T cells both reduces terminal exhaustion and enhances T cell effector responses (i.e. IFN-{gamma} and granzyme production) to chronic infection and cancer. Together, these results establish the KEAP1-NRF2 axis as a metabolic sensor linking oxidative stress to CD8 T cell dysfunction and identify the prostacyclin receptor PTGIR as an NRF2-regulated immune checkpoint that regulates CD8 T cell fate decisions between effector and exhausted states. One Sentence SummaryThe KEAP1-NRF2 pathway is hyperactivated in terminally exhausted CD8 T cells and drives T cell dysfunction via transcriptional regulation of the prostacyclin receptor, Ptgir.

immunology↗

Complex compositional and cellular response of river sediment microbiomes to multiple anthropogenic stressors

Rivers face constant anthropogenic stressors, resulting in significant changes in microbial community composition. What remains unclear is whether these changes render the microbiome better adapted to the stressed environment. Here, by subjecting 64 river-connected mesocosms to multiple stressors, we show that sediment microbiomes of small lowland rivers are highly sensitive to lowered flow velocity resulting in substantially altered community compositions not fully capable of compensating for the stressor effect within two weeks albeit having stable functions encoded in metagenomes. Transcriptomics revealed a systematic heat shock response in the community and a highly active, previously unknown anaerobic key stone species with great metabolic versatility. Increases in temperature (+3.5 {degrees}C) or salinity (+0.5 mS/cm) were outcompeted by lowered flow and elicited only minor responses at community or transcriptomic level with, e.g., upregulation of the photosystem of chloroplasts. Following a two-week recovery period, transcriptomic stress responses vanished completely compared to control mesocosms, exemplifying the river microbiomes resilience. We conclude that, given the complex community responses at both the cellular and compositional level, maintaining natural river flow is vital to preventing energy loss and reduced microbiome activity in river sediments.

ecology↗

Conjugation mediates large-scale chromosomal transfer in Streptomyces driving diversification of antibiotic biosynthetic gene clusters

Streptomyces are ubiquitous soil dwelling bacteria of special importance as a source of metabolites used in human and veterinary medicine, agronomy and industry. Conjugation is the main mechanism of Streptomyces Horizontal Gene Transfer, and this process has long been known to be accompanied by mobilization of chromosomal DNA. However, the magnitude of DNA transfer, or the localization of acquired DNA across their linear chromosome, has remained undetermined. We here show that conjugative crossings in sympatric strains of Streptomyces result in the large-scale, genome-wide distributed replacement of up to one third of the recipient chromosome, a phenomenon for which we propose the name Streptomyces Chromosomal Transfer (SCT). Such chromosome blending results in the acquisition, loss and hybridization of Specialized Metabolite Biosynthetic Gene Clusters, leading to a novel metabolic arsenal in exconjugant offspring. Harnessing conjugation-mediated SMBGC diversification holds great promise in the discovery of new bioactive compounds including antibiotics.

microbiology↗

Macroevolutionary dynamics in micro-organisms: generalists give rise to specialists across biomes in the ubiquitous bacterial phylum Myxococcota.

Prokaryotes dominate the Tree of Life, but our understanding of the macroevolutionary processes generating this diversity is still limited. Habitat transitions are thought to be a key driver of prokaryote diversity, but we still know relatively little about how prokaryotes successfully transition and persist across environments, and how this varies between biomes and lineages. Here, we investigate biome transitions and specialisation in natural populations of a focal bacterial phylum, the Myxococcota, sampled across a range of replicated soils and freshwater and marine sediments in Cornwall (UK). By targeted deep sequencing of the protein-coding gene rpoB, we found >2000 unique Myxococcota lineages, with the majority (77%) being biome specialists and <5% able to live across the salt barrier. Discrete character evolution models revealed that biome specialists very rarely transitioned to specialising in another biome. Instead, generalists mediated transitions between biome specialists. Multistate hidden-state speciation and extinction models found variation in speciation rate across the tree, but this variation was independent of biome association and specialisation. Overall, our results help explain how microbes transition between biomes and are consistent with "the jack-of-all-trades" trade-off, where generalists suffer a cost in any individual environment, resulting in rapid evolution of niche specialists.

microbiology↗

13C metabolite tracing reveals glutamine and acetate as critical in vivo fuels for CD8+ T cells

Infusion of 13C-labeled metabolites provides a gold-standard for understanding the metabolic processes used by T cells during immune responses in vivo. Through infusion of 13C-labeled metabolites (glucose, glutamine, acetate) in Listeria monocytogenes (Lm)-infected mice, we demonstrate that CD8+ T effector (Teff) cells utilize metabolites for specific pathways during specific phases of activation. Highly proliferative early Teff cells in vivo shunt glucose primarily towards nucleotide synthesis and leverage glutamine anaplerosis in the tricarboxylic acid (TCA) cycle to support ATP and de novo pyrimidine synthesis. Additionally, early Teff cells rely on glutamic-oxaloacetic transaminase 1 (Got1)--which regulates de novo aspartate synthesis--for effector cell expansion in vivo. Importantly, Teff cells change fuel preference over the course of infection, switching from glutamine-to acetate-dependent TCA cycle metabolism late in infection. This study provides insights into the dynamics of Teff metabolism, illuminating distinct pathways of fuel consumption associated with Teff cell function in vivo. TeaserInterrogating dynamics of fuel utilization by CD8+ T cells in vivo reveals new metabolic checkpoints for immune function in vivo.

immunology↗

Copper reduces the virulence of bacterial communities at environmentally relevant concentrations

Increasing environmental concentrations of metals as a result of anthropogenic pollution are significantly changing many microbial communities. While there is evidence metal pollution can result in increased antibiotic resistance, the effects of metal pollution on virulence remains largely undetermined. Here, we experimentally test whether metal stress alters the virulence of bacterial communities. We do this by incubating three wastewater influent communities under different environmentally relevant copper concentrations for three days. We then quantify the virulence of the community using the Galleria mellonella infection model, and test if differences are due to changes in the rate of biomass accumulation (productivity), copper resistance, or community composition (quantified using 16S amplicon sequencing). The virulence of the communities was found to be reduced by the highest copper concentration, but not to be affected by the lower concentration. As well as reduced virulence, communities exposed to the highest copper concentration were less diverse and had lower productivity. This work highlights that metal pollution may decrease virulence in bacterial communities, but at a cost to diversity and productivity.

microbiology↗

Cryo-EM and Molecular Dynamics Simulations Reveal Hidden Conformational Dynamics Controlling Ammonia Transport in Human Asparagine Synthetase

How motions in enzymes might be linked to catalytic function is of considerable general interest. Advances in X-ray crystallography and cryogenic electron microscopy (cryo-EM) offer the promise of elucidating functionally relevant conformational changes that are not easily studied by other biophysical methods. Here we use 3D variability analysis (3DVA) of the cryo-EM map for wild-type (WT) human asparagine synthetase (ASNS) to identify a functional role for the Arg-142 side chain as a gate that mediates ammonia access to a catalytically relevant intramolecular tunnel. Our 3DVA-derived hypothesis is assessed experimentally, using the R142I variant in which Arg-142 is replaced by isoleucine, and by molecular dynamics (MD) simulations on independent, computational models of the WT human ASNS monomer and its catalytically relevant, ternary complex with {beta}-aspartyl-AMP and MgPPi. Residue fluctuations in the MD trajectories for the human ASNS monomer are consistent with those determined for 3DVA-derived structures. These MD simulations also indicate that the gating function of Arg-142 is separate from the molecular events that form a continuous tunnel linking the two active sites. Experimental support for Arg-142 playing a role in intramolecular ammonia translocation is provided by the glutamine-dependent synthetase activity of the R142 variant relative to WT ASNS. MD simulations of computational models for the R142I variant and the R142I/{beta}-aspartyl-AMP/MgPPi ternary complex provide a possible molecular basis for this observation. Overall, the combination of 3DVA with MD simulations is a generally applicable approach to generate testable hypotheses of how conformational changes in buried side chains might regulate function in enzymes.

molecular biology↗

The effect of metal remediation on the virulence and antimicrobial resistance of the opportunistic pathogen Pseudomonas aeruginosa

Metal contamination poses both a direct threat to human health as well as an indirect threat through its potential to affect bacterial pathogens. Metals can not only co-select for antibiotic resistance, but also might affect pathogen virulence via increased siderophore production. Siderophores are extracellular compounds released to increase ferric iron uptake -- a common limiting factor for pathogen growth within hosts - making them an important virulence factor. However, siderophores can also be positively selected for to detoxify non-ferrous metals, and consequently metal stress can potentially increase bacterial virulence. Anthropogenic methods to remediate environmental metal contamination commonly involve amendment with lime-containing materials, but whether this reduces in situ co-selection for antibiotic resistance and virulence remains unknown. Here, using microcosms containing metal-contaminated river water and sediment, we experimentally test whether metal remediation by liming reduces co-selection for these traits in the opportunistic pathogen Pseudomonas aeruginosa embedded within a natural microbial community. To test for the effects of environmental structure, which can impact siderophore production, microcosms were incubated under either static or shaking conditions. Evolved P. aeruginosa populations had greater fitness in the presence of toxic concentrations of copper than the ancestral strain, but this effect was reduced in the limed treatments. Evolved P. aeruginosa populations showed increased resistance to the clinically-relevant antibiotics apramycin, cefotaxime, and trimethoprim, regardless of lime addition or environmental structure. Although we found virulence to be significantly associated with siderophore production, neither virulence nor siderophore production significantly differed between the four treatments. We therefore demonstrate that although remediation via liming reduced the strength of selection for metal resistance mechanisms, it did not mitigate metal-imposed selection for antibiotic resistance or virulence in P. aeruginosa. Consequently, metal-contaminated environments may select for antibiotic resistance and virulence traits even when treated with lime. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/508257v2_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@2f396corg.highwire.dtl.DTLVardef@62e7b3org.highwire.dtl.DTLVardef@159d269org.highwire.dtl.DTLVardef@52395_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗