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Biology subjects

Dijkstra, J.

Publications and source records attributed to Dijkstra, J..

11 recordsLinked to original sources

Stressed Overwintering Bottleneck Hypothesis: Ocean warming and acidification synergistically disrupt Arctic zooplankton overwintering

Ocean warming (OW), driven by the influx of warm Atlantic water masses, and acidification (OA) are threatening Arctic marine ecosystems. However, their potential synergistic effects are poorly understood, especially during the Polar Night when marine species are particularly vulnerable to stressors. Here, we tested our novel Stressed Overwintering Bottleneck Hypothesis (SOBH): warming will disrupt the overwintering of the keystone pan-Arctic copepod Calanus glacialis, a pivotal secondary producer, by impairing fitness-related traits underpinning survival and reproduction. We exposed C. glacialis to current and projected future OW levels (0 {degrees}C and 4 {degrees}C) and OA levels (pH 8.0 and 7.4-7.3) for 53 days during the mid-Arctic Polar Night. We assessed survival, development, and physiological and molecular mechanisms (oxygen consumption, lipid depletion, the expression of nine targeted genes related to oxidative stress and damage repair, and DNA damage). OW alone did not affect C. glacialis mortality; however, OA increased copepod survival at 0 {degrees}C. Notably, their combined effects (OWA) synergistically doubled mortality, as predicted by SOBH. Warming also accelerated moulting from copepodite stage V to adulthood in December, and increased respiration, exhausted lipid reserves entirely by early March, approximately one to four months before the spring algal bloom, further supporting SOBH. DNA damage and gene expression patterns indicated low investment in maintenance and damage repair. Collectively, these findings reveal hidden mechanisms by which OW and OA synergistically threaten overwintering Calanus copepods by drastically increasing mortality, accelerating moulting, raising metabolic rates, and causing early lipid depletion. These effects generate cross-seasonal phenological mismatches among overwintering survival, energy reserves, reproduction, and primary production. Such stressed overwintering bottlenecks in foundational secondary producers like Calanus copepods provide novel explanations for how OW and OA can constrict Arctic marine food webs. At a broader perspective, SOBH highlights how multiple stressors induced overwintering disruption could reshape pan-Arctic and global biodiversity.

ecology↗

A meta-analysis of 3-nitrooxypropanol effects on methane production and yield in beef cattle

Beef cattle are a major source of enteric methane (CH4) emissions, a potent greenhouse gas (GHG). The feed additive 3-nitrooxypropanol (3-NOP) has been shown to reduce CH4 emissions by inhibiting methyl-coenzyme M reductase, an enzyme critical to methanogenesis in archaea. This study aimed to quantify the effects of 3-NOP on CH4 production (g/d) and yield (g/kg DM intake; DMI) in beef cattle and to evaluate how diet composition influences the mitigation response. A systematic literature review identified 17 peer-reviewed in vivo studies, yielding 45 treatment means. Treatment effects were expressed as absolute and relative mean differences versus control groups. Predictor variables included 3-NOP dose, 3-NOP dose2, DMI, dietary concentration of NDF, CP, starch, fat, and organic matter (OM), roughage proportion, BW, and dietary inclusion of monensin (yes/no). Four types of models were developed, all including the intercept and 3-NOP dose as fixed predictors, differing as follows: (model 1) optional inclusion of 3-NOP dose2 when P < 0.10; (model 2) model 1 plus pre-inclusion of NDF concentration; (model 3) pre-inclusion of NDF concentration plus additional predictors (pairwise r [&le;] 0.5) that significantly improved model accuracy (P < 0.10); and (model 4) additional predictors selected under the same criteria as model 3, without pre-inclusion of NDF concentration. For models 3 and 4, a maximum of 5 predictors were considered and evaluated using leave-one-out cross-validation. Across studies, 3-NOP doses ranged from 32 to 338 mg/kg of DM. On average, 3-NOP reduced CH4 production by 49.9 {+/-} 28.61 g/d (36.2 {+/-} 24.42%) and CH4 yield by 5.3 {+/-} 3.61 g/kg DMI (33.2 {+/-} 25.54%). The best models were selected based on biological interpretability, statistical significance, and predictive accuracy (as measured by RMSE) and included 3-NOP dose, dietary NDF concentration, DMI, and BW as significant predictors (the latter two only for absolute CH4 production). Mitigation efficacy increased with higher DMI and declined with increasing NDF concentration and BW. Absolute reductions of 53.1 g/d and 5.88 g/kg of DMI, and relative reductions of 37.6% in CH4 production and 35.0% in CH4 yield were predicted when moderators were at their mean value (3-NOP dose = 134.4 mg/kg of DM; NDF concentration = 32.8% of DM; DMI of 8.6 kg/d). These results support the effectiveness of 3-NOP in mitigating enteric CH4 emission in beef cattle and provide quantitative models to be used in assessment tools and GHG inventory methodology. ImplicationsThe feed additive 3-nitrooxypropanol effectively reduces enteric methane emissions in beef cattle. This meta-analysis found average reductions of 36.2% in methane production and 33.2% in methane yield. Efficacy depended on diet composition; declining with increasing NDF concentration for both methane production (g/d) and yield (g/kg of DM intake; DMI). Greater DMI increased absolute methane production reduction but did not influence absolute methane yield reduction or relative reduction of both methane production and yield. These results support the targeted use of 3-nitrooxypropanol as a mitigation strategy and provide empirical models to inform greenhouse gas inventories and carbon accounting.

systems biology↗

Habitat suitability modeling growth and cover trends of staghorn coral (Acropora cervicornis) outplants in the lower Florida Keys

The decline of important reef building corals has motivated the development of habitat suitability models used to identify optimal locations for coral restoration. In the Florida Keys habitat suitability models incorporate coarse spatial data sampled over large areas, resulting in recommended outplant sites at distant locations, making it logistically difficult and expensive to access and regularly monitor. Restoration efforts to date show that outplanting success can vary widely within a limited space, necessitating improved predictive abilities of coral outplant success at high spatial resolutions within a restoration site. With the advent of Structure-from-Motion image reconstruction, fine-scale, site specific, digital terrain models can be created to support habitat suitability model development. In this study, generalized linear mixed models used extracted seafloor terrain attributes and environmental variables to identify within site locations of high Acropora cervicornis growth and healthy coral cover of long-term outplants. Percent healthy coral cover significantly decreased after two years of outplantation. The submodel of corals exclusively less than two years old was unable to identify environmental conditions associated with higher healthy cover. For all corals, outplant recommendations for higher healthy cover are in deeper waters, away from the coast, in less rough terrain, and closer to the reef edge. Model results for growth support these recommended outplant sites, in addition to concave locations near high slope relief. Finally, our results also indicate that marine heat waves, but especially marine cold waves negatively correspond with coral growth, and high wind events positively correspond with coral growth. These model results provide a basis for further endeavors in modeling endangered organismal success, which are vulnerable to minute differences in local environmental conditions.

ecology↗

A meta-analysis of effects of seaweed and other bromoform containing feed ingredients on methane production, yield, and intensity in cattle

Methane (CH4) emissions from ruminants contribute significantly to global GHG emissions. Bromoform (CHBr3)-containing feed ingredients, such as Asparagopsis seaweed, have emerged as promising tools to reduce enteric CH4 emissions. This meta-analysis quantitatively assessed the effects of CHBr3-containing seaweeds and synthetic CHBr3-based additives on CH4 production (g/day), CH4 yield (g/kg DMI), and DMI, as well as CH4 intensity (g/kg product) and production (milk or daily gain in dairy and beef cattle, respectively). Data were collected from 14 studies, with 39 treatment mean differences for CH4 production, comprising both beef and dairy cattle fed CHBr3-containing ingredients, while accounting for dose, DMI, and diet composition. The random-effects models estimates revealed that at an average CHBr3 dose of {approx}28.3 mg/kg DM, CH4 production was reduced by 47.3%, CH4 yield by 43.3%, and CH4 intensity by 39.0%, with increases in CHBr3 dose resulting in larger efficacy in mitigating CH4 emissions. The efficacy of CHBr3 was influenced by cattle type, with greater mitigation effects in beef cattle than dairy catle, and by dietary composition, with greater reductions observed in diets higher in starch, whereas higher NDF levels attenuate its effect. At the average CHBr3 dose, estimated DMI was significantly reduced by 6.45% and 3.26% in dairy and beef cattle, respectively. The significant reduction in DMI did translate into a significant effect on milk yield (-4.60%) at average CHBr3 dose. Carrier type (oil vs. biomass), measurement technique and cattle type influenced the results. Oil carrier potentially leading to more pronounced reductions, particularly for CH4 intensity, respiration chambers yielded significantly greater CH4 reductions compared to other methods, and beef cattle showed stronger mitigation effects than dairy cattle. This study highlights the CH4 mitigating potential of CHBr3-containing feed ingredients, providing predictive models to optimize CH4 reduction strategies under diverse production conditions. Future research should address long-term effects, dietary optimization, and practical implementation.

systems biology↗

Transposon activity eliminates a crucial fungal secondary metabolite cluster while preserving pathogenicity

SummaryO_LITransposable elements can significantly influence the genome dynamics of clonal fungal plant pathogens. Tropical Race 4 (TR4) is a clonal lineage within the Fusarium oxysporum species complex that poses a substantial threat to global banana production. However, how transposable elements shape TR4s genome and adaptation remains underexplored. C_LIO_LIWe investigated the activity and impact of FoHeli1, a Helitron transposable element in the TR4 lineage, focusing on a Mozambican TR4 strain (M1) through a combination of genome analyses, metabolite profiling, and infection assays. C_LIO_LIFoHeli1 activity has been very recent within the TR4 lineage and is likely still ongoing. This has resulted in large structural variations in M1, including the loss of the conserved biosynthetic gene cluster required for the production of fusaric acid. We demonstrate that this deletion abolishes fusaric acid production and alters secondary metabolite profiles, but does not affect pathogenicity. C_LIO_LIOur results emphasize the significance of transposable elements, particularly FoHeli1, in reshaping the genetic and metabolic landscape of TR4 and challenge existing assumptions about the role of fusaric acid in pathogenicity. C_LI

microbiology↗

Extensive intrachromosomal duplications in a virulence-associated fungal accessory chromosome

Filamentous fungi have evolved compartmentalized genomes consisting of conserved core regions and dynamic accessory regions, which aid the adaptation to changing environments including the interaction with host organisms. In the Fusarium oxysporum species complex, accessory regions play an important role during infection and it has been reported that these regions undergo extensive duplications, however, it is currently unknown how such duplications shape accessory regions. Moreover, the function of accessory regions apart from encoding virulence effectors is not completely understood. Here we determined the karyotype of F. oxysporum Tropical Race 4 (TR4), which causes the ongoing pandemic of Fusarium wilt of banana (FWB). We show that the single accessory chromosome of TR4 isolate II5 has undergone extensive intrachromosomal duplications, resulting in triplication of the chromosome size compared to other closely related TR4 strains. By obtaining mutant strains that have lost the accessory chromosome, we demonstrate that this chromosome is dispensable for vegetative growth but is required for full virulence on banana. Lastly, we found that the loss of chromosome 12 co-occurs with structural rearrangements of core chromosomes, which are generally co-linear between members of the F. oxysporum species complex. Together, our results provide new insights into the chromosome dynamics of the banana infecting TR4 lineage of the F. oxysporum species complex. SignificanceFusarium oxysporum is a major fungal plant pathogen that causes vascular wilt disease on a wide variety of agronomically important crops. A current epidemic of Fusarium wilt of banana (FWB), caused by tropical race 4 (TR4), poses a major threat to global banana production and threatens food security in tropical and subtropical regions where banana is an important staple crop. Controlling TR4 requires a better understanding of the molecular mechanisms underlying pathogenicity, including the evolution of pathogenicity-related accessory regions. Here we demonstrate that intrachromosomal duplications are a key mechanism of accessory chromosome evolution in the F. oxysporum species complex. We identified a single accessory chromosome and show that TR4 mutants that lost this accessory chromosome display significantly reduced virulence on banana plants. Our results provide insight into the evolution of accessory chromosomes in the F. oxysporum species complex, underscore their importance in pathogenicity, and provide new clues for the development of resistant banana plants.

microbiology↗

Frequent genetic exchange shapes the pan-mitogenome of the fungal plant pathogen Fusarium oxysporum

Mitochondria are present in almost all eukaryotic lineages. The mitochondrial genomes (mitogenomes) evolve separately from nuclear genomes, and they can therefore provide relevant insights into the evolution of their host species. Fusarium oxysporum is a major fungal plant pathogen that is assumed to reproduce clonally. However, horizontal chromosome transfer between strains can occur through heterokaryon formation, and recently signs of sexual recombination have been observed. Similarly, signs of recombination in F. oxysporum mitogenomes challenged the prevailing assumption of clonal reproduction in this species. Here, we construct, to our knowledge, the first fungal pan-mitogenome graph of nearly 500 F. oxysporum mitogenome assemblies to uncover the variation and evolution. In general, the gene order of fungal mitogenomes is not well conserved, yet the mitogenome of F. oxysporum and related species are highly co-linear. We observed two strikingly contrasting regions in the Fusarium oxysporum pan-mitogenome, comprising a highly conserved core mitogenome and a long variable region (6-16 kb in size), of which we identified three distinct types. The pan-mitogenome graph reveals that only five intron insertions occurred in the core mitogenome and that the long variable regions drive the difference between mitogenomes. Moreover, we observed that their evolution is neither concurrent with the core mitogenome nor with the nuclear genome. Our large-scale analysis of long variable regions uncovers frequent recombination between mitogenomes, even between strains that belong to different taxonomic clades. This challenges the common assumption of incompatibility between genetically diverse F. oxysporum strains and provides new insights into the evolution of this fungal species. Importance statementInsights into plant pathogen evolution is essential for the understanding and management of disease. Fusarium oxysporum is a major fungal pathogen that can infect many economically important crops. Pathogenicity can be transferred between strains by the horizontal transfer of pathogenicity chromosomes. The fungus has been thought to evolve clonally, yet recent evidence suggests active sexual recombination between related isolates, which could at least partially explain the horizontal transfer of pathogenicity chromosomes. By constructing a pan-genome graph of nearly 500 mitochondrial genomes, we describe the genetic variation of mitochondria in unprecedented detail and demonstrate frequent mitochondrial recombination. Importantly, recombination can occur between genetically diverse isolates from distinct taxonomic clades and thus can shed light on genetic exchange between fungal strains.

genomics↗

Segmental Duplications Drive the Evolution of Accessory Regions in a Major Crop Pathogen

O_LIMany pathogens evolved compartmentalized genomes with conserved core and variable accessory regions which carry effector genes mediating virulence. The fungal plant pathogen Fusarium oxysporum has such accessory regions often spanning entire chromosomes. The presence of specific accessory regions influences the host range, and horizontal transfer of some accessory regions can modify the pathogenicity of the receiving strain. However, understanding how these accessory regions evolve in strains that infect the same host remains limited. C_LIO_LIHere, we define the pan-genome of 69 diverse Fusarium strains that cause Fusarium wilt of banana, a significant constraint to global banana production. In this diverse panel of Fusarium strains infecting banana, we analyzed the diversity and evolution of the accessory regions. C_LIO_LIAccessory regions in Fusarium strains infecting the same banana cultivar are highly diverse, and we could not identify any shared genomic regions and in planta induced effectors. We demonstrate that segmental duplications drive the evolution of accessory regions. Furthermore, we show that recent segmental duplications and aneuploidy occur specifically in accessory chromosomes and cause the expansion of accessory regions in F. oxysporum. C_LIO_LITaken together we conclude that extensive recent duplications drive the evolution of accessory regions in Fusarium, which contribute to the evolution of virulence. C_LI

genomics↗

Comparison of shear stress patterns by the established and advanced reconstruction method incorporating side branches to predict plaque progression

BackgroundComplete vessel reconstruction (CVR) with incorporation of side branches is essential for accurate evaluation of wall shear stress (WSS) distribution. However, CVR is time consuming and blood flow simulation is computationally expensive, while there is no evidence that WSS computed by CVR, enables better prediction of disease progression compared to WSS derived from the conventional single vessel reconstruction (SVR). We aim to compare the WSS in models reconstructed using the CVR and SVR methods and examine its ability to predict disease progression. MethodsPatients who had baseline and 13-months follow-up intravascular ultrasound (IVUS) imaging (n=19 vessels), and with neoatherosclerotic lesions (n=13 vessels) on optical coherence tomography (OCT) were included in the present analysis. All the studied vessels had at least one side branch with diameter >1mm. 3-dimensional (3D) CVR and SVR were performed and time averaged (TAWSS) and multidirectional WSS were computed using pulsatile blood flow simulation and the performance of both methods in predicting disease progression in IVUS and OCT models were assessed. ResultsThe incorporation of side branches in 3D geometry resulted in lower TAWSS in the IVUS (0.821 vs 1.698Pa, p<0.001) and OCT-based reconstructions (0.682 vs 1.325Pa, p<0.001) and influenced the multidirectional WSS distribution. In native segments, WSS metrics estimated by the CVR enabled better prediction of the lumen and plaque area and burden at follow-up than SVR and disease progression defined as decrease in lumen area and increase in plaque burden (AUC CVR 0.712 vs SVR 0.554). In stented segments, multidirectional WSS was associated with neointima area in both CVR and SVR methods, but TAWSS was only a predictor of neointima area in the CVR method. ConclusionsThe incorporation of side branches in vessel reconstruction influences WSS distribution and enables more accurate prediction of disease progression in native and stented segments than SVR modelling. HighlightsO_LIComplete vessel reconstruction (CVR) with incorporation of vessel side branches has been proposed for accurate evaluation of wall shear stress (WSS) distribution compared to the traditional single vessel reconstruction (SVR) method; however, there are no studies comparing the performance of the WSS metrics derived by these methods in predicting atherosclerotic evolution. C_LIO_LIIn vessels with large side branches, the incorporation of the side branches in the vessel geometry reconstructed from angiographic and intravascular imaging data resulted in lower time averaged wall shear stress (TAWSS) and influenced the multidirectional WSS estimations compared to the models reconstructed without the side branches. C_LIO_LIThe WSS metrics estimated in the CVR models enabled better prediction of atherosclerotic disease progression at 13-months follow-up on IVUS than the WSS derived by the SVR. C_LIO_LIIn stented vessels, all the WSS metrics in the CVR and the multidirectional WSS in SVR were associated with neointima tissue development; however, both approaches showed limited efficacy in predicting neointima proliferation. C_LI

bioengineering↗

THRONCAT: Efficient metabolic labeling of newly synthesized proteins using a bioorthogonal threonine analog

Profiling the nascent cellular proteome and capturing early proteomic changes in response to external stimuli provides valuable insight into cellular physiology. Existing metabolic protein labeling approaches based on bioorthogonal methionine-or puromycin analogs allow for the selective visualization and enrichment of the newly synthesized proteins. However, their applications are limited as they require methionine-free conditions, auxotrophic cells and/or are toxic to cells. Here, we introduce THRONCAT, a novel threonine-derived non-canonical amino acid tagging method based on bioorthogonal threonine analog {beta}-ethynylserine ({beta}ES) that enables efficient and non-toxic labeling of the nascent proteome in complete growth media within minutes. We used THRONCAT for the visualization and enrichment of nascent proteins in bacteria, mammalian cells and Drosophila melanogaster. We profiled immediate proteome dynamics of Ramos B-cells in response to receptor activation, demonstrating the ease-of-use of the method and its potential to address diverse biological questions. In addition, using a Drosophila model of Charcot-Marie-Tooth peripheral neuropathy, we show that THRONCAT enables visualization and quantification of relative protein synthesis rates in vivo.

cell biology↗

Iron-loading is a prominent feature of activated microglia in Alzheimer's disease patients

Brain iron accumulation has been found to accelerate disease progression in Amyloid {beta}-positive Alzheimer patients, though the mechanism is still unknown. Microglia have been identified as key-players in the disease pathogenesis, and are highly reactive cells responding to aberrations such as increased iron levels. Therefore, using histological methods, multispectral immunofluorescence and an automated in-house developed microglia segmentation and analysis pipeline, we studied the occurrence of iron-accumulating microglia and the effect on its activation state in human Alzheimer brains. We identified a subset of microglia with increased expression of the iron storage protein ferritin light chain (FTL), together with increased Iba1 expression, decreased TMEM119 and P2RY12 expression. This activated microglia subset represented iron-accumulating microglia and appeared morphologically dystrophic. Multispectral immunofluorescence allowed for spatial analysis of FTL+Iba1+-microglia, which were found to be the predominant A{beta}-plaque infiltrating microglia. Finally, an increase of FTL+Iba1+-microglia was seen in patients with high Amyloid-{beta} load and Tau load. These findings suggest iron to be taken up by microglia and to influence the functional phenotype of these cells, especially in conjunction with A{beta}.

neuroscience↗