Biology subjects

Bakker, J.

Publications and source records attributed to Bakker, J..

15 recordsLinked to original sources

bioRxiv2026

A repair-associated bronchial epithelial differentiation trajectory through KRT14+ basal and hillock-like cells drives airway inflammation and remodelling in childhood-onset asthma

The bronchial epithelium in asthma is vulnerable to damage and has impaired barrier function, but the mechanisms by which it contributes to airway inflammation and remodelling remain unclear. Here, we dissect these epithelial and immunological disease mechanisms by establishing a comprehensive single cell atlas of the bronchial wall from 21 patients with childhood-onset asthma and 25 matched healthy controls. We identify a novel asthma-associated non-canonical epithelial differentiation trajectory in which a repair-associated KLF4+ basal cell subset differentiates into KRT13+ hillock-like cells through a proliferative KRT14+ intermediate. In vitro cultured matched primary bronchial epithelial cells show that this trajectory is retained in absence of exogenous factors. We find that IL-13 induces hillock-like cell differentiation into CEACAM5hi goblet cells, driving goblet cell metaplasia. Repair-associated basal cells and transitioning CEACAM5hi hillock-like cells strongly contribute to airway inflammation and remodelling. In turn, dendritic cells and mast cells promote a state of highly active epithelial differentiation, which shows increased multiciliated cell fate decisions, in concordance with an increase in multiciliated cell death observed in asthma. Proportions of the epithelial cells of the non-canonical differentiation trajectory are associated with clinical outcomes such as disease severity, FeNO, and small airway function.

immunology↗

bioRxiv2026

Intra-annual precipitation variability mutes or magnifies the impact of wet and dry years on plant biomass.

As the atmosphere warms, both the amount and timing of precipitation are changing, but how those two trends interact to influence plant growth remains unresolved. Using 5-15 years of data from 48 globally distributed grassland sites, we quantified how the temporal distribution of precipitation within the year (evenness) interacts with annual precipitation amount and nutrient limitation to influence plant biomass. Annual precipitation anomalies had a large influence on plant biomass when intra-annual precipitation was more evenly distributed (frequent small events) and little impact when less even (infrequent large events). This relationship was consistent across aridity gradients and nutrient limitations and strongest in systems with warm wet seasons. Our work shows that the response of plant systems to changes in annual precipitation amount are largely dependent on how evenly it is temporally distributed.

ecology↗

bioRxiv2025

High cell-type specificity of eQTLs revealed by single-nucleus analyses of brain and blood

Identifying causal mechanisms from genome-wide association studies (GWAS) requires an understanding of how disease-associated genetic variants influence gene expression in specific cell types. Here, we present scMetaBrain, a large-scale single-nucleus RNA-sequencing (snRNA-seq) resource derived using 1,260 samples from 785 individuals spanning 10 brain datasets. By analyzing 3.9 million transcriptomes, we identified 19,371 unique expression quantitative trait locus (eQTL) genes (eGenes) at a major cell type level, with the largest number of eQTLs observed in excitatory neurons. Notably, 31% of the eQTLs detected were highly cell-type-specific, with most restricted to excitatory neurons (69%). We compared the eQTLs with bulk RNA-seq datasets across different tissues and with a newly generated single nucleus dataset of 123 donors from peripheral blood mononuclear cells. We observed that differences in eQTL effect sizes between brain cell types are often as large as comparing eQTLs between brain tissue and non-brain tissue from bulk RNA-seq studies. Furthermore, we observe that eQTL effect size agreement was highest for cell types with similar function, even when comparing brain to blood cells. This suggests that that bulk analyses substantially overestimate eQTL agreement, likely due to tissue-level averaging of cellular regulatory effects. Through colocalization, we prioritized 662 genes for 11 brain-related traits and prioritized a single cell type in 68% of genes. Our findings demonstrate that eQTL effects are far more cell-type-specific than previously recognized, underscoring the need to expand single-cell eQTL studies across diverse tissues and cell types to fully capture the regulatory architecture of genetic variants.

genetics↗

bioRxiv2025

Evolution-assisted engineering of formate assimilation via the formyl phosphate route in Escherichia coli

The transition towards a sustainable bioeconomy requires the use of alternative feedstocks, with CO2-derived formate emerging as a promising candidate for industrial biotechnology. Despite its beneficial characteristics as a feedstock, microbial assimilation of formate is limited by the inefficiency of naturally evolved formate-fixing pathways. To overcome this limitation, synthetic formate reduction cascades could enable formate assimilation via formaldehyde, a key intermediate of several existing one carbon assimilation pathways. Recently, the formyl phosphate route, combining ATP-dependent activation of formate to formyl phosphate, followed by its reduction to formaldehyde, was developed through enzyme engineering and characterized in vitro. In this work, we successfully established the formyl phosphate route in vivo by developing a selection strategy that couples formate reduction to growth in a threonine/methionine auxotrophic Escherichia coli. Through adaptive laboratory evolution, we achieved formate-dependent growth via this novel pathway. Evolved strains were capable of growing robustly with formate concentrations between 20 mM and 100 mM with glucose in the co-feed. Genomic and proteomic analyses together with activity assays uncovered that formate activation was limiting in vivo. This discovery guided the rational engineering of a strain capable of efficient formate assimilation through the formyl phosphate route. By demonstrating that novel enzyme activities can link formate reduction to cell growth, our study shows how synthetic metabolic routes can be functionally established inside the cell, paving the way for the engineering of more complex synthetic pathways.

bioengineering↗

bioRxiv2024

Long-term non-trophic effects of large herbivores on plant diversity are underestimated

The positive effects of large herbivores on plant diversity in grasslands have so far been mainly attributed to increased light availability or suppressed dominance, and thus to the consequences of aboveground biomass consumption (trophic effects). However, these insights are mainly derived from short-term experiments. Using a 46-year experiment in a salt marsh, comparing cattle grazing, mowing (as a proxy of aboveground consumption) and the ungrazed control, we found that the non-trophic effects (e.g. trampling, deposition of urine and dung) of large herbivores on plant diversity increased over time, exceeding that of the trophic effects after 23 years. This long-term accumulation of non-trophic effects through slow ecosystem-level feedback highlights the sustainability of using low to moderate densities of large herbivores to conserve plant diversity. Our results emphasize the need for the conservation and re-introduction of large herbivores, domestic or wild, to sustain long-term grassland plant diversity.

ecology↗

bioRxiv2024

The repetitive genome of the Ixodes ricinus tick reveals transposable elements have driven genome evolution in ticks

Ticks are obligate blood-feeding parasites associated with a huge diversity of diseases globally. The hard tick Ixodes ricinus is the key vector of Lyme borreliosis and tick-borne encephalitis in Western Eurasia. Ixodes ticks have large and repetitive genomes that are not yet well characterized. Here we generate two high-quality I. ricinus genome assemblies, with haploid genome sizes of approximately 2.15 Gbp. We find transposable elements comprise at least 69% of the two I. ricinus genomes, amongst the highest proportions found in animals. The transposable elements in ticks are highly diverse and novel, so we constructed a repeat library for ticks using our I. ricinus genomes and the genome of I. scapularis, another major tick vector of Lyme borreliosis. To understand the impact of transposable elements on tick genomes we compared their accumulation in the two Ixodes sister species. We find transposable elements in these two species to be drivers of genome evolution in ticks. The I. ricinus genome assemblies and our tick repeat library will be valuable resources for biological insights into this important ectoparasite. Our findings highlight that further research into the impact of transposable elements on the genomes of blood-feeding parasites is required.

genomics↗

bioRxiv2023

The lung extracellular matrix protein landscape in severe early-onset and moderate chronic obstructive pulmonary disease.

Extracellular matrix (ECM) remodeling has been implicated in the irreversible obstruction of airways and destruction of alveolar tissue in chronic obstructive pulmonary disease (COPD). Studies investigating differences in the lung ECM in COPD have mainly focused on some collagens and elastin, leaving an array of ECM components unexplored. We investigated the differences in the ECM landscape comparing severe-early onset (SEO-) COPD and moderate COPD to control lung tissue for collagen type I chain 1 (COL1A1), COL6A1, COL6A2, COL14A1, fibulin 2 and 5 (FBLN2, FBLN5), latent transforming growth factor-beta binding protein 4 (LTBP4), lumican (LUM), versican (VCAN), decorin (DCN), and elastin (ELN) using image analysis and statistical modelling. Percentage area and/or mean intensity of expression of LUM in the parenchyma, and COL1A1, FBLN2, LTBP4, DCN, and VCAN in the airway walls, was proportionally lower in COPD compared to controls. Lowered levels of most ECM proteins were associated with decreasing FEV1 measurements, indicating a relationship with disease severity. Furthermore, we identified six unique ECM signatures where LUM and COL6A1 in parenchyma and COL1A1, FBLN5, DCN, and VCAN in airway walls appear essential in reflecting the presence and severity of COPD. These signatures emphasize the need to examine groups of proteins to represent an overall difference in the ECM landscape in COPD, that are more likely to be related to functional effects, than individual proteins. Our study revealed differences in the lung ECM landscape between control and COPD and between SEO and moderate COPD signifying distinct pathological processes in the different subgroups. NEW & NOTEWORTHYOur study identified COPD-associated differences in the lung ECM composition. We highlight the compartmental differences in the ECM landscape in different subtypes of COPD. The most prominent differences were observed for severe-early onset COPD. Moreover, we identified unique ECM signatures that describe airway walls and parenchyma providing insight into the intertwined nature and complexity of ECM changes in COPD that together drive ECM remodeling and may contribute to disease pathogenesis.

molecular biology↗

bioRxiv2023

WOX11-mediated adventitious lateral root formation modulates tolerance of Arabidopsis to cyst nematode infections

The transcription factor WUSCHEL-RELATED HOMEOBOX 11 (WOX11) in Arabidopsis initiates the formation of adventitious lateral roots upon mechanical injury in primary roots. Root-invading nematodes also induce de novo root organogenesis leading to excessive root branching, but it is not known if this symptom of disease involves mediation by WOX11 and if it benefits the plant. Here, we show with targeted transcriptional repression and reporter gene analyses in Arabidopsis that the beet cyst nematode Heterodera schachtii activates WOX11-adventitious lateral rooting from primary roots close to infection sites. The activation of WOX11 in nematode-infected roots occurs downstream of jasmonic acid-dependent damage signaling via ETHYLENE RESPONSIVE FACTOR109, linking adventitious lateral root formation to nematode damage to host tissues. By measuring different root system components, we found that WOX11-mediated formation of adventitious lateral roots compensates for nematode-induced inhibition of primary root growth. Our observations further demonstrate that WOX11-mediated rooting reduces the impact of nematode infections on aboveground plant development and growth. Altogether, we conclude that the transcriptional regulation by WOX11 modulates root system plasticity under biotic stress, which is one of the key mechanisms underlying tolerance of Arabidopsis to cyst nematode infections.

plant biology↗

bioRxiv2023

Design, construction and optimization of formaldehyde growth biosensors with broad application in Biotechnology

Formaldehyde is a key metabolite in natural and synthetic one-carbon metabolism as well as an important environmental toxin with high toxicity at low concentrations. To engineer efficient formaldehyde producing enzymes and to detect formaldehyde in industrial or environmental samples, it is important to establish highly sensitive, easy to use and affordable formaldehyde detection methods. Here, we transformed the workhorse bacterium Escherichia coli into biosensors that can detect a broad range of formaldehyde concentrations. Based on natural and promiscuous formaldehyde assimilation enzymes, we designed and engineered three different E. coli strains that depend on formaldehyde assimilation for cellular growth. After in depth characterization of these biosensors, we show that the formaldehyde sensitivity can be improved through adaptive laboratory evolution or modification of metabolic branch points. The metabolic engineering strategy presented in this work allowed the creation of E. coli biosensors that can detect formaldehyde in a concentration range from [~]30 M to [~]13 mM. Using the most sensitive strain, we benchmarked the in vivo activities of different, widely used NAD-dependent methanol dehydrogenases, the rate-limiting enzyme in synthetic methylotrophy. We also show that the strains can grow upon external addition of formaldehyde indicating their potential use for applications beyond enzyme engineering. The formaldehyde biosensors developed in this study are fully genomic and can be used as plug and play devices for screening large enzyme libraries. Thus, they have the potential to greatly advance enzyme engineering and might even be used for environmental monitoring or analysis of industrial probes. Highlights- Conversion of E. coli into three different formaldehyde growth biosensors - Biosensors are fully genomic and grow robustly when formaldehyde is present - Biosensors can detect formaldehyde concentrations ranging from [~]30 M to [~]13 mM - Benchmarking of biotechnological relevant methanol dehydrogenases reveals potential of biosensors for enzyme engineering - Biosensors grow upon direct addition of formaldehyde indicating potential use in environmental or industrial settings

bioengineering↗

bioRxiv2023

Cross-species comparison of pregnancy-induced GDF15

GDF15 (growth differentiation factor 15) is a stress-induced cytokine. Although the exact physiological function of GDF15 is not yet fully comprehended, the significant elevation of circulating GDF15 levels during gestation suggests a potential role for this hormone in pregnancy. This is corroborated by genetic association studies in which GDF15 and the GDF15 receptor, GDNF Family Receptor Alpha Like (GFRAL) have been linked to morning sickness and hyperemesis gravidarum (HG) in humans. Here, we studied GDF15 biology during pregnancy in mice, rats, macaques, and humans. In contrast to macaques and humans, mice and rats exhibited an underwhelming induction in plasma GDF15 levels in response to pregnancy ([~]75-fold increase in macaques vs. [~]2-fold increase in rodents). The changes in circulating GDF15 levels were corroborated by the magnitude of Gdf15 mRNA and GDF15 protein expression in placentae from mice, rats, and macaques. These species-specific findings may help guide future studies focusing on GDF15 in pregnancy and on the evaluation of pharmacological strategies to interfere with GDF15-GFRAL signaling to treat severe nausea and HG.

physiology↗

bioRxiv2021

Bronchoalveolar lavage affects thorax computed tomography of healthy and SARS-CoV-2 infected rhesus macaques (Macaca mulatta)

Medical imaging as method to assess the longitudinal process of a SARS-CoV-2 infection in non-human primates is commonly used in research settings. Bronchoalveolar lavage (BAL) is also regularly used to determine the local virus production and immune effects of SARS-CoV-2 in the lower respiratory tract. However, the potential interference of those two diagnostic modalities with each other is unknown in non-human primates. The current study investigated the effect and duration of BAL on computed tomography (CT) in both healthy and experimentally SARS-CoV-2-infected female rhesus macaques (Macaca mulatta). In addition, the effect of subsequent BALs was reviewed. Thorax CTs and BALs were obtained from four healthy animals and 11 experimentally SARS-CoV-2-infected animals. From all animals, CTs were obtained just before BAL, and 24 hours post-BAL. Additionally, from the healthy animals, CTs immediately after and four hours post-BAL were obtained. Thorax CTs were evaluated for alterations in lung density, measured in Hounsfield units, and a visual semi-quantitative scoring system. An increase in the lung density was observed on the immediately post-BAL CT but resolved within 24 hours in the healthy animals. In the infected animals, a significant difference in both the lung density and CT score was still found 24 hours after BAL. Furthermore, the differences between timepoints in CT score were increased for the second BAL. These results indicate that the effect of BAL on infected lungs is not completed within the first 24 hours. Therefore, it is of importance to acknowledge the interference between BAL and CT in rhesus macaques.

biophysics↗

bioRxiv2020

Topoisomerase 1 inhibition therapy protects against SARS-CoV-2-induced inflammation and death in animal models.

The ongoing pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is currently affecting millions of lives worldwide. Large retrospective studies indicate that an elevated level of inflammatory cytokines and pro-inflammatory factors are associated with both increased disease severity and mortality. Here, using multidimensional epigenetic, transcriptional, in vitro and in vivo analyses, we report that Topoisomerase 1 (Top1) inhibition suppresses lethal inflammation induced by SARS-CoV-2. Therapeutic treatment with two doses of Topotecan (TPT), a FDA-approved Top1 inhibitor, suppresses infection-induced inflammation in hamsters. TPT treatment as late as four days post-infection reduces morbidity and rescues mortality in a transgenic mouse model. These results support the potential of Top1 inhibition as an effective host-directed therapy against severe SARS-CoV-2 infection. TPT and its derivatives are inexpensive clinical-grade inhibitors available in most countries. Clinical trials are needed to evaluate the efficacy of repurposing Top1 inhibitors for COVID-19 in humans.

microbiology↗

bioRxiv2020

Conserved codon adaptation in highly expressed genes is associated with higher regularity in mRNA secondary structures

The redundancy of the genetic code allows for a regulatory layer to optimize protein synthesis by modulating translation and degradation of mRNAs. Patterns in synonymous codon usage in highly expressed genes have been studied in many species, but scarcely in conjunction with mRNA secondary structure. Here, we analyzed over 2,000 expression profiles covering a range of strains, treatments, and developmental stages of five model species (Escherichia coli, Arabidopsis thaliana, Saccharomyces cerevisiae, Caenorhabditis elegans, and Mus musculus). By comparative analyses of genes constitutively expressed at high and low levels, we revealed a conserved shift in codon usage and predicted mRNA secondary structures. Highly abundant transcripts and proteins, as well as high protein per transcript ratios, were consistently associated with less variable and shorter stretches of weak mRNA secondary structures (loops). Genome-wide recoding showed that codons with the highest relative increase in highly expressed genes, often C-ending and not necessarily the most frequent, enhanced formation of uniform loop sizes. Our results point at a general selective force contributing to the optimal expression of abundant proteins as less variable secondary structures promote regular ribosome trafficking with less detrimental collisions, thereby leading to an increase in mRNA stability and a higher translation efficiency.

bioinformatics↗

bioRxiv2020

The germline mutational process in rhesus macaque and its implications for phylogenetic dating

Understanding the rate and pattern of germline mutations is of fundamental importance for understanding evolutionary processes. Here we analyzed 19 parent-offspring trios of rhesus macaques (Macaca mulatta) at high sequencing coverage of ca. 76X per individual, and estimated an average rate of 0.77 x 10-8 de novo mutations per site per generation (95 % CI: 0.69 x 10-8 - 0.85 x 10-8). By phasing 50 % of the mutations to parental origins, we found that the mutation rate is positively correlated with the paternal age. The paternal lineage contributed an average of 81 % of the de novo mutations, with a trend of an increasing male contribution for older fathers. About 3.5 % of de novo mutations were shared between siblings, with no parental bias, suggesting that they arose from early development (postzygotic) stages. Finally, the divergence times between closely related primates calculated based on the yearly mutation rate of rhesus macaque generally reconcile with divergence estimated with molecular clock methods, except for the Cercopithecidae/Hominoidea molecular divergence dated at 52 Mya using our new estimate of the yearly mutation rate.

evolutionary biology↗

bioRxiv2017

GM-CSF negatively regulates early IL-10 mediated responses

Inflammatory disorders are becoming more prevalent in the Western world. Treatment of these diseases relies on the intervention in inflammatory responses thereby restoring immune homeostasis. One cytokine that has the potential to restore immune homeostasis is the anti-inflammatory cytokine interleukin-10 (IL-10). But until now IL-10 treatment has not been as successful as anticipated. A reason for this may be that IL-10 responsiveness depends on the environment of the inflamed tissue. In this study we describe that granulocyte-macrophage colony-stimulating factor (GM-CSF) is a key cytokine that negatively regulates IL-10-mediated responses. Dendritic cells differentiated from bone marrow with GM-CSF have a reduced ability to respond to IL-10. Dendritic cells are impaired in their up-regulation of IL-10-induced SOCS3 expression and are unable to suppress LPS-induced TNF- expression at an early time point. Furthermore, GM-CSF treatment partially replicates this phenotype in macrophages. Surprisingly, GM-CSF seems to regulate IL-10 activity in macrophages without affecting STAT3 activation. Still, GM-CSF induces constitutive phosphorylation of glycogen synthase kinase 3{beta}, a signalling component downstream of the PI3K/Akt pathway. Knowledge on the exact mechanism by which GM-CSF negatively regulates IL-10 activity could give novel insights on the integration of signal transduction pathways elicited by different cytokines. Ultimately this knowledge could provide us with new therapeutic strategies to treat inflammatory disorders.

immunology↗