Biology subjects

Jonsson, M.

Publications and source records attributed to Jonsson, M..

12 recordsLinked to original sources

bioRxiv2026

Leaf litter decomposition, microbial respiration and community succession under variable dissolved organic carbon availability in boreal streams

Boreal forested streams receive substantial inputs of terrestrial carbon (C) from riparian vegetation in the form of leaf litter, which is processed by litter-associated microorganisms. In addition to these leaf-litter C inputs, boreal streams also receive significant concentrations of dissolved organic carbon (DOC), which may represent an alternative major resource pool for litter-associated microorganisms. As leaf litter quality decreases over the process of decomposition, DOC may increasingly become a more suitable C source for the microbial communities. We investigated how DOC availability, litter type, and microbial succession influenced respiration and decomposition. Alder, birch, and spruce litter were incubated for 65 days in 12 outdoor experimental channels supplied with natural boreal stream water. Higher time-adjusted DOC concentrations were associated with higher respiration and lower relative mass remaining, whereas DOC flux received less support. Respiration and mass loss followed litter-specific trajectories, with birch showing a respiration peak that was not matched by proportional mass loss. Prokaryotic and eukaryotic communities differed among litter types and changed through time but explained process variation only for specific litter types and responses. Our results suggest that DOC can sustain litter-associated microbial activity and partly decouple respiration from litter decomposition, thereby affecting boreal stream C processing.

ecology↗

bioRxiv2026

Fermentation of the Edible Brown Seaweed Alaria esculenta by Lactiplantibacillus plantarum affects nutritional prfile and the content of potentially toxic elements.

Edible seaweed has the potential to become a valuable marine resource for food applications due to its potential health benefits and ecological sustainability. The brown seaweed Alaria esculenta is rich in essential minerals, vitamins, and dietary fibers, making it a nutritious food source. Fermentation, as a traditional preservation method, can enhance seaweed shelf-life and be useful for the development of new foods/ beverages. In this study, the effects of fermentation of A. esculenta, by the lactic acid bacterium (LAB) Lactiplantibacillus plantarum, on the nutritional profile, and the content of potentially toxic elements, was investigated. L. plantarum was successfully cultivated on A. esculenta using two modes of operation, submerged (SmF) and solid-state fermentation (SSF), resulting in production of cells and lactic acid, and reduction of the pH to below 4.3 within 3 days, which was not achieved in parallel spontaneous fermentations using indigenous seaweed microbiota. A. esculenta s macro-nutritional profile was altered, reducing mannitol but increasing fucose and glucose content (after acid hydrolysis) while also concentrating the protein content. LAB fermentation significantly increased the concentration of antioxidant phenolic compounds, such as phloroglucinol, syringic acid, and epicatechin, compared to untreated samples. However, lipophilic compounds like carotenoids decreased after both spontaneous and LAB-fermentation. A reduction in total mineral content was observed after LAB fermentation and water soaking, and SmF with L. plantarum effectively reduced arsenic and iodine levels. Overall, fermentation using L. plantarum showed potential as a bio-preservation method for the edible brown seaweed, A. esculenta, improving its nutritional profile and enhancing food safety.

microbiology↗

bioRxiv2026

Extrafollicular plasma cells disable dendritic cell-T-cell priming in tumor-draining lymph nodes

How plasma cells (PCs) shape anti-tumor immunity is unclear. We hypothesized that conflicting prognostic associations reflect differences in immune context and PC ontogeny. We identify extrafollicular (EF)-PCs as an antibody-independent checkpoint that aborts priming by disabling the cDC1[->]CD8+ T-cell axis in tumor-draining lymph nodes (td-LNs). EF-PCs blunt cDC1 activation and CCR7-guided repositioning into T-cell zones, precluding formation of TCF1 stem-like CD8 T-cells. Depleting EF-PCs in vivo restores cDC1 trafficking, expands the stem-like reservoir, increases intratumoral CD8 infiltration, and restrains tumor growth; benefit is lost with CD8 T-cell ablation. Neither serum transfer nor Fc{gamma} receptor blockade reverses tumor control, supporting a non-canonical, antibody-independent mechanism. Across independent triple-negative breast cancer cohorts, we find EF-PC hyperplasia in td-LNs and tumors; and within immune-cold cases, EF-PC burden stratifies poor prognosis and metastatic risk. A cross-species EF-PC signature maps to a conserved PC-state across cancer types that is linked to poor outcome and immune-checkpoint blockade resistance. EF-PCs thus relocate the dominant failure point to td-LNs and offer a tractable upstream target to convert immune-cold tumors into immune-responsive disease.

immunology↗

bioRxiv2025

Diverging drivers of alpha and beta diversity across management types in Swedish boreal forests

O_LIManaging multifunctional forest landscapes requires a better understanding of how biodiversity dimensions respond to habitat structures and management regimes. While species richness is commonly used to assess conservation value, it may not capture compositional differences critical for maintaining regional biodiversity. C_LIO_LIWe examined how local species richness (alpha diversity) and community turnover (beta diversity) relates to forest structure and management in Swedish boreal forests. We surveyed lichens, bryophytes, and polypore fungi, representing three sessile taxo-ecological groups across 120 sites.. The sites were distributed between three management types: young production forests, retention patches (trees left during harvest to support mature forest species in production forests), and unmanaged set-asides. We used generalised linear models and generalised dissimilarity modelling to assess how habitat structures (deadwood and living tree metrics) and spatial distance explained patterns of richness and turnover across taxa and management types. C_LIO_LIFor all taxa, species richness increase with lying deadwood volume. Lichen species richness also increased with living tree volume, and decreased with tree density in retention patches. Lichens had higher species richness in retention patches and set-asides, whereas only set-asides had statistically higher bryophyte richness, and there were no differences for polypore richness. In contrast, beta diversity was more often associated with geographic distance, with only limited influence of deadwood volume. The relationships between lichen beta diversity and habitat structures were not consistent between retention patches and set-asides, suggesting that retention patches may have limitations in conserving mature forest species despite supporting similar lichen species richness. C_LIO_LISynthesis and applications. Our results demonstrate that alpha and beta diversity can be driven by different ecological processes and management contexts, and that while tree retention can support higher biodiversity than young production forests in some taxa, it cannot replace the value of conserving mature forests. Effective conservation therefore needs to combine habitat quality and spatial complementarity when planning conservation initiatives to maintain diversity patterns across managed landscapes. C_LI

ecology↗

bioRxiv2023

Seasonal tissue-specific gene expression reveals reproductive and stress-related transcriptional systems in wild crown-of-thorns starfish

Animals are influenced by the season, yet we know little about the changes that occur in most species throughout the year. This is particularly true in tropical marine animals that experience relatively small annual temperature and daylight changes. Like many coral reef inhabitants, the crown-of-thorns starfish (COTS), well known as a notorious consumer of corals and destroyer of coral reefs, reproduces exclusively in the summer. By comparing gene expression in seven somatic tissues procured from wild COTS sampled on the Great Barrier Reef, we identified more than 2,000 protein-coding genes that change significantly between summer and winter. COTS genes that appear to mediate conspecific communication - including both signalling factors released into the surrounding sea water and cell surface receptors - are upregulated in external secretory and sensory tissues in the summer, often in a sex-specific manner. The sexually dimorphic gene expression appears to be underpinned by sex- and season-specific transcription factors (TFs) and gene regulatory programs. There are over 100 TFs that are seasonally expressed, 86% of which are significantly upregulated in the summer. Six nuclear receptors are upregulated in all tissues in the summer, suggesting that systemic seasonal changes are hormonally controlled, as occurs in vertebrates. Unexpectedly, there is a suite of stress-related chaperone proteins and TFs, including HIF, ATF3, C/EBP, CREB and NF-{kappa}B, that are uniquely co-expressed in gravid females. The upregulation of these stress proteins in the summer suggests the demands of oogenesis in this highly fecund starfish affects protein stability and turnover in somatic cells. Together, these circannual changes in COTS gene expression provide novel insights into seasonal changes in this coral reef pest and have the potential to identify vulnerabilities for targeted biocontrol.

zoology↗

bioRxiv2023

Understanding and exploitation of host stress responses to protein production using novel transcriptomic analytics

Predictable expression of heterologous genes in a production host is a fundamental challenge in biotechnology. While traditional methods focus on manipulating expression and the property of the heterologous gene, a systems biology approach can complement with designs to improve the host itself. Previously, Independent Component Analysis (ICA) of the RNAseq data helped reveal independently modulated gene sets (iModulons) in bacteria. This was later applied to identify common stress responses related to heterologous gene expression for Escherichia coli. In this study, we expand this analysis with additional non-enzymatic proteins and apply our findings to design novel protein production optimization. By leveraging the Precise-1K transcriptomics knowledge base, we identify three iModulons as novel transcriptional responses to protein production stress; Cold Shock, gcvB sRNA, and the uncharacterized UC-9 iModulons. By studying the gene membership in the UC-9 iModulon, we discover effective novel design targets for improving protein production. This study demonstrates the value of big data analytics and systems understanding of host responses for designing novel strategies to optimize protein production.

systems biology↗

bioRxiv2022

Crown-of-thorns starfish in captivity experience sustained large-scale changes in gene expression

Marine animals in the wild are often difficult to access, so that biologists have to extrapolate from the study of animals in captivity. However, the implicit assumption that physiological and cellular processes of animals in artificial environments are not significantly different from those in the wild has rarely been tested. Here we investigate the extent to which the biological state of an animal is impacted by captivity by comparing global gene expression in wild and captive crown-of-thorns starfish (COTS). We compare transcriptomes of three external tissues obtained from wild COTS with captive COTS maintained in aquaria for at least one week. On average, an astonishingly large 24% of the coding sequences in the genome are differentially expressed. Comparing transcriptomes from coelomocytes - cells in internal coelomic fluid - in wild and captive COTS, we find that 20% of the coding sequences in the genome rapidly change expression. These captive transcriptomes remained markedly different from the wild ones for more than 30 days in captivity, and showed no indication of reverting back to a wild state. Genes consistently upregulated in captivity include those involved in oxidative stress and energy metabolism, whereas genes downregulated are involved in intercellular signalling. These extensive changes in gene expression in captive COTS suggest that captivity has a profound and sustained impact on the physiology, behaviour and health of these echinoderms. The potential for such dramatic changes should be accounted for when designing studies seeking to understand wild animals.

molecular biology↗

bioRxiv2021

Long noncoding RNA VENTHEART is required for cardiomyocyte specification and function

RationaleLong noncoding RNAs (lncRNAs) control cardiac gene expression during heart development and disease. It is accordingly plausible for the same lncRNA to regulate both cardiac development, as well as play a role in adult heart disease progression. lncRNA regulators of early cardiomyocyte (CM) lineage commitment have been identified and characterised, however those controlling later CM specification remain unknown. ObjectivesIn this study we identified a novel lncRNA required for CM specification, maturation and function, and also discovered its suggested relevance to heart disease. Methods and ResultsWe performed single cell RNA-seq on human embryonic stem cell derived cardiomyocytes at 2, 6 and 12 weeks of differentiation. Weighted correlation network analysis (WGCNA) identified core gene modules, including lncRNAs highly abundant and uniquely expressed in the human heart. A lncRNA (we call VENTHEART, VHRT) co-expressed with cardiac maturation and ventricular-specific genes MYL2 and MYH7, as well as in adult human ventricular tissue. CRISPR-mediated excision of VHRT led to impaired CM sarcomere formation, and loss of the CM specification gene program. VHRT knockdown (KD) in hESC-CMs confirmed its regulatory role for key cardiac contraction, calcium hemostasis and heart development genes, including MYH6 and RYR2. Functional evaluation after VHRT KD using impedance-based technology and action potential recordings, proved reduced contraction amplitude and loss of the ventricular-like action potential in CM, respectively. Through an integrative analysis of genome-wide association studies (GWAS), expression quantitative trait locus (eQTL) and gene co-expression network, we found VHRT to be co-regulated with core cardiac contractile genes, and the likely source of a heart failure genetic association signal overlapping the VHRT gene locus. Finally, VHRT KD and human failing heart transcriptome comparison validates the consistent downregulation again of cardiac contractile and calcium regulatory genes (P<0.05). ConclusionWe conclude that VHRT lncRNA is required for proper CM specification and function. Furthermore, reduced VHRT may contribute to the development or progression of human heart disease.

cell biology↗

bioRxiv2020

Reducing ecological complexity using the archetype approach - an application to natural pest control

Natural control of crop pests has the potential to complement or replace intensive agricultural practices, but its mainstream application requires reliable predictions in diverse socioecological settings. In lack of a widely accepted model of natural pest control, we review existing modelling approaches and critically examine their potential to provide understanding and predictions across agricultural landscapes. Models that explicitly represent the underlying mechanisms are better positioned to represent the diversity and context sensitivity of natural pest control than correlative models. Such mechanistic models have used diverse techniques to represent crop-pest-enemy combinations at various spatiotemporal scales. However, certain regions of the world and socioeconomic aspects of natural pest control are underrepresented, while modelling approaches are restricted by a fundamental trade-off between generality and realism. We propose that modelling natural pest control across agroecosystems requires a framework of context-specific generalizations, based on empirical evidence and theoretical expectations. Reviewed models of natural pest control indicate potential attributes of such a general predictive framework.

ecology↗

bioRxiv2019

Just how big is intraspecific trait variation in fungal fruit bodies?

As the use of functional trait approaches is growing in fungal ecology, there is a corresponding need to understand trait variation. Much of trait theory and statistical techniques are built on the assumption that interspecific variation is larger than intraspecific variation. This allows the use of mean trait values for species, which the vast majority of trait studies adopt. We examined the size of intra- vs. inter-specific variation in two wood fungal fruit body traits: size and density. Both coefficients of variation (CV) and Trait Probability Density analyses were used to quantify trait variation. We found that intraspecific variation in fruit body density was more than twice as variable as interspecific variation, and fruit body size was hugely variable (CVs averaged 190%), although interspecific variation was larger. Further, there was a very high degree of overlap in the trait space of species, indicating that there may be little niche partitioning at the species level. These findings show that intraspecific variation is highly important and should be accounted for when using trait approaches to understand fungal ecology. More data on variation of other fungal traits is also desperately needed to ascertain whether the high level of variation found here is typical for fungi. While the need to measure individuals does reduce the ability to generalise at the species level, it does not negate the usefulness of fungal trait measurements. There are two reasons for this: first, the ecology of most fungal species remains poorly known and trait measurements address this gap; and secondly, if trait overlap between species more generally is as much as we found here, then individual measurements may be more helpful than species identity for untangling fungal community dynamics.

ecology↗

bioRxiv2019

A global synthesis reveals biodiversity-mediated benefits for crop production

Human land use threatens global biodiversity and compromises multiple ecosystem functions critical to food production. Whether crop yield-related ecosystem services can be maintained by few abundant species or rely on high richness remains unclear. Using a global database from 89 crop systems, we partition the relative importance of abundance and species richness for pollination, biological pest control and final yields in the context of on-going land-use change. Pollinator and enemy richness directly supported ecosystem services independent of abundance. Up to 50% of the negative effects of landscape simplification on ecosystem services was due to richness losses of service-providing organisms, with negative consequences for crop yields. Maintaining the biodiversity of ecosystem service providers is therefore vital to sustain the flow of key agroecosystem benefits to society.

ecology↗

bioRxiv2017

From Cohorts to Molecules: Adverse Impacts of Endocrine Disrupting Mixtures

Convergent evidence associates endocrine disrupting chemicals (EDCs) with major, increasingly-prevalent human disorders. Regulation requires elucidation of EDC-triggered molecular events causally linked to adverse health outcomes, but two factors limit their identification. First, experiments frequently use individual chemicals, whereas real life entails simultaneous exposure to multiple EDCs. Second, population-based and experimental studies are seldom integrated. This drawback was exacerbated until recently by lack of physiopathologically meaningful human experimental systems that link epidemiological data with results from model organisms.\n\nWe developed a novel approach, integrating epidemiological with experimental evidence. Starting from 1,874 mother-child pairs we identified mixtures of chemicals, measured during early pregnancy, associated with language delay or low-birth weight in offspring. These mixtures were then tested on multiple complementary in vitro and in vivo models. We demonstrate that each EDC mixture, at levels found in pregnant women, disrupts hormone-regulated and disease-relevant gene regulatory networks at both the cellular and organismal scale.

molecular biology↗