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Biology subjects

Jensen, C.

Publications and source records attributed to Jensen, C..

At least 19 recordsLinked to original sources

Collagen type I promotes pancreatic tumor growth and limits immune cell infiltration

Solid tumors are often characterized by a dense extracellular matrix (ECM) that contributes to increased tissue stiffness. Collagen type I is the main component of the ECM and its abundance in tumors is frequently associated with poor prognosis. In vitro studies suggest that a high collagen density promotes tumor invasion and modulates immune responses. However, recent in vivo findings have questioned the pro-tumorigenic role of collagen type I. In this study, we investigate the role of collagen for pancreatic tumor growth and immune cell infiltration using conditional collagen type I knockout mice and transgenic collagenase-resistant mice. Preventing collagen type I significantly reduces intratumoral collagen content and tumor growth. This reduction is accompanied increased infiltration of natural killer (NK) cells, a higher CD8/CD4 T cell ratio, and decreased numbers of monocytic myeloid-derived suppressor cells (MDSCs). Conversely, collagenase-resistant mice develop collagen-dense tumors and display enhanced tumor growth. These mice also generally exhibit opposing effects on cell infiltration, including a lower CD8/CD4 ratio and increased MDSC abundance. These findings are further supported by analyses of publicly available human cancer datasets, which confirm an association between collagen type I levels and immune cell infiltration. Overall, our results demonstrate a pronounced pro-tumorigenic role of collagen type I in pancreatic cancer, which is associated with modulation of the tumor immune microenvironment. This study highlights the importance of extracellular matrix components as key regulators of tumor progression and anti-tumor immunity.

cancer biology↗

Iterative and modular expression of Botryococcus braunii genes enhances isoprenoid production in the diatom Phaeodactylum tricornutum

Isoprenoids are essential natural compounds with high structural and functional diversity. Among them, carotenoids and triterpenoids such as squalene have high biotechnological value but remain challenging to produce sustainably. The green microalga Botryococcus braunii synthesizes large amounts of triterpenoids through specialized methylerythritol phosphate (MEP) pathway configurations involving distinct 1-deoxy-D-xylulose-5-phosphate synthase (DXS) isoforms, a bifunctional squalene synthase (SQS) and squalene synthase-like (SSL) enzymes working together for the synthesis of the compound. However, its slow growth limits industrial application. In this work, we established the fast-growing diatom Phaeodactylum tricornutum as a heterologous chassis for terpenoid production using a synthetic biology Design-Build-Test-Learn (DBTL)-based approach. Episomal uLoop assembly enabled rapid expression and evaluation of B. braunii DXS and SQS variants, enhancing precursor flux and resulting in the co-accumulation of squalene and carotenoids. This work demonstrates the functional transfer of specialized algal terpenoid enzymes into a tractable diatom host and highlight P. tricornutums potential as a versatile platform for sustainable, high-value isoprenoid biosynthesis.

synthetic biology↗

Chemical proteomics decrypts the kinases that shape the dynamic human phosphoproteome

Mass-spectrometry-based phosphoproteomics enables the analysis of thousands of protein phosphorylation events across the human proteome. However, there is a lack of scalable, hypothesis-free, and statistically sound approaches for discovering, evaluating, and falsifying kinase::substrate relationships (KSRs). Here, we developed a new concept termed potency-coherence analysis. By measuring and integrating 17 million peptidoform-specific dose-response curves for 133 kinase inhibitors with known targets and affinities, we could critically re-evaluate published KSRs and discover thousands of potency-coherent and motif-plausible new KSRs for 96 human kinases. Application of these high-confidence KSRs enabled the estimation of kinase and signaling pathway activities in cancer patient biopsies. This unified and extendable framework has been implemented in ProteomicsDB to aid researchers in understanding the human phosphoproteome in health and disease.

systems biology↗

Yorzoi: Predicting RNA-seq coverage from DNA sequence in yeast

Yeast is one of the principal model organisms in synthetic biology and a widely used chassis for testing heterologous DNA sequences. However, designing DNA constructs correctly is currently limited by our incomplete quantitative understanding of how sequences are transcribed and translated, especially non-native sequences. Here, we present Yorzoi, a sequence-to-expression model for bakers yeast that predicts RNA-seq coverage for a 5 kilobase, multi-gene window of DNA at 10 base pair (bp) resolution. To extend its predictive ability beyond native DNA, Yorzoi has been pretrained on a comprehensive dataset not only including native yeast sequences but also human sequences expressed in yeast and structurally rearranged synthetic yeast chromosomes. We demonstrate that our model has learned general rules of yeast transcription by achieving high predictive performance on various downstream tasks. Yorzoi is a powerful tool for in-silico testing of DNA sequences and directly applicable for sequence design. A web application to use our model is available at yorzoi.eu and the code open source on GitHub.

synthetic biology↗

A key role for Canoes intrinsically disordered region in linking cell junctions to the cytoskeleton

AbstractAdherens junctions are key to tissue architecture, mediating robust yet dynamic cell-cell adhesion and, via cytoskeletal linkage, allowing cells to change shape and move. Adherens junctions contain thousands of molecules linked by multivalent interactions of folded protein domains and Intrinsically Disordered Regions (IDRs). One key challenge is defining mechanisms conferring robust linkage and mechanosensing. Drosophila Canoe and mammalian Afadin provide superb entrypoints to explore how their complex protein structures and shared IDRs enable function. We combined genetic, cell biological and biochemical tools to define how Canoes IDR functions during morphogenesis. Unlike many of Canoes folded domains, the IDR is critical for junctional localization, mechanosensing and function. We took the IDR apart, identifying two conserved stickers in the IDR that directly bind F-actin, separated by less-conserved spacers. Surprisingly, while mutants lacking the IDR die as embryos with morphogenesis defects, no sub-region of the IDR is essential for viability. Instead, IDR stickers and spacers act combinatorially to ensure localization, mechanosensing and function.

cell biology↗

Effects of Unexpected Underfoot Perturbations During Turning on Measures of Mediolateral Stability and Corresponding Recovery Strategies

Humans regularly walk across uneven terrain, which demands the use of reactive control strategies to maintain forward progress and stability. While reactive control during walking has been well described during straight gait, it is unclear how reactive control differs during turning gait. Because turning is asymmetrical, perturbations to the inside and outside limbs may elicit different reactive adjustments. This study investigates how unexpected underfoot perturbations alter stability measures during turning and how individuals alter their foot placement to maintain stability after such perturbations. Seven healthy adults completed walking trials around a circular track while wearing mechanized shoes that pseudo-randomly delivered underfoot perturbations to either the inside or outside limb. We calculated mediolateral margin of stability corrected for centripetal acceleration (ML MoSC), step width, and step length from kinematic data. Linear mixed effects models compared the effects of perturbation type (inversion vs eversion), perturbation limb (inside vs outside), and their interaction for each outcome measure. ML MoSC was affected by both perturbation type and perturbation limb, with larger changes observed during eversion, and outside, perturbations. Changes to step width and step time during two recovery steps after each perturbation were primarily influenced by the perturbation limb - outside perturbations elicited consistent changes during two recovery steps compared to one altered step after inside perturbations. Perturbations to the outside limb during turning disrupt gait longer than perturbations to the inside limb. This difference across perturbation limb may indicate that outside steps are more important to maintaining and recovering stability than inside ones during turning.

bioengineering↗

Winter temperature effects in a cold-adapted northern population of a range-expanding spider: survival, energy stores, and differential gene expression

Species expand their spatial distribution when environmental conditions are favorable or when mutations arise that allow them to live in previously unfavorable conditions. The European wasp spider, Argiope bruennichi, is known to have expanded its range poleward faster than climate change would predict. Northern edge populations show higher cold tolerance and are genetically differentiated from core populations, suggesting local adaptation to colder winter conditions. To investigate the degree and limits of plasticity in a cold-adapted population, we exposed overwintering juveniles (spiderlings) from Estonia - the northern edge of the distribution - to three winter regimes: two with a strong difference in day/night temperatures and an overall 10 degrees difference (warm and cold treatment) and one with moderate temperatures and less difference between day and night (moderate). We investigated if survival, lipid content, metabolites, and gene expression patterns differ depending on these temperature regimes. The survival probability of the spiderlings and their overall lipid content decreased over winter, with no difference between treatments, suggesting high resilience of the spiderlings towards very different temperature regimes at the edge of the distribution. At the end of winter, the content of saturated and monounsaturated fatty acids per spiderling also did not differ between treatments. However, omega-3 polyunsaturated fatty acids (PUFAs) levels were significantly lower in spiders exposed to the warm winter suggesting increased metabolic activity. We identified 4096 significant differentially expressed genes (DEGs) across the treatments, of which 1389 were specific for the moderate treatment, and 832 specific for the warm treatment, while 69 were unique for the cold treatment, showing a stronger temperature stress response to the moderate and warmer than to the cold treatment. Taken together, our results show that A. bruennichi has physiological plasticity and the ability to cope with very different winter temperature regimes despite being cold adapted. However, warmer winters might come with metabolic costs that could impact on the spiderling[s] survival and foraging success when they emerge from the egg sac in spring.

ecology↗

The dual Ras Association (RA) Domains of Drosophila Canoe have differential roles in linking cell junctions to the cytoskeleton during morphogenesis

During embryonic development and adult homeostasis epithelial cells must change shape and move without disrupting the tissues dynamic architecture. This requires robust linkage of cell-cell adherens junctions to the force-generating actomyosin cytoskeleton. Drosophila Canoe and mammalian Afadin play key roles in this linkage. One central task for the field is defining how upstream inputs from Ras-family GTPases regulate Canoe and Afadin. They are unusual in that they share two tandem Ras-association (RA) domains, which, when deleted, virtually eliminate Canoe function. Previous work in vitro suggested RA1 and RA2 differ in their ability to bind GTPases, but their individual functions in vivo remain unknown. Combining bioinformatic and biochemical approaches, we find that both RA1 and RA2 bind to active Rap1 with similar affinities, and that conserved N-terminal extensions play a role in binding. We created Drosophila canoe mutants to test RA1 and RA2 function in vivo. Despite their similar affinities for Rap1, RA1 and RA2 play strikingly different roles. Deleting RA1 virtually eliminates Canoe function in morphogenesis, while mutants lacking RA2 are viable and fertile but have defects in junctional reinforcement in embryos and during pupal eye development. These data significantly expand our understanding of how adherens junction:cytoskeletal linkage is regulated.

cell biology↗

nf-core/airrflow: an adaptive immune receptor repertoire analysis workflow employing the Immcantation framework

Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) is a valuable experimental tool to study the immune state in health and following immune challenges such as infectious diseases, (auto)immune diseases, and cancer. Several tools have been developed to reconstruct B cell and T cell receptor sequences from AIRR-seq data and infer B and T cell clonal relationships. However, currently available tools offer limited parallelization across samples, scalability or portability to high-performance computing infrastructures. To address this need, we developed nf-core/airrflow, an end-to-end bulk and single-cell AIRR-seq processing workflow which integrates the Immcantation Framework following BCR and TCR sequencing data analysis best practices. The Immcantation Framework is a comprehensive toolset, which allows the processing of bulk and single-cell AIRR-seq data from raw read processing to clonal inference. nf-core/airrflow is written in Nextflow and is part of the nf-core project, which collects community contributed and curated Nextflow workflows for a wide variety of analysis tasks. We assessed the performance of nf-core/airrflow on simulated sequencing data with sequencing errors and show example results with real datasets. To demonstrate the applicability of nf-core/airrflow to the high-throughput processing of large AIRR-seq datasets, we validated and extended previously reported findings of convergent antibody responses to SARS-CoV-2 by analyzing 97 COVID-19 infected individuals and 99 healthy controls, including a mixture of bulk and single-cell sequencing datasets. Using this dataset, we extended the convergence findings to 20 additional subjects, highlighting the applicability of nf-core/airrflow to validate findings in small in-house cohorts with reanalysis of large publicly available AIRR datasets. Availability and implementationnf-core/airrflow is available free of charge, under the MIT license on GitHub (https://github.com/nf-core/airrflow). Detailed documentation and example results are available on the nf-core website at (https://nf-co.re/airrflow). Visual abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC="FIGDIR/small/576147v2_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@e39504org.highwire.dtl.DTLVardef@14c52aforg.highwire.dtl.DTLVardef@1c87664org.highwire.dtl.DTLVardef@1d4d78b_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

Biochemical activity is the default DNA state in eukaryotes

Genomes encode for genes and the regulatory signals that enable those genes to be transcribed, and are continually shaped by evolution. Genomes, including those of human and yeast, encode for numerous regulatory elements and transcripts that have limited evidence of conservation or function. Here, we sought to create a genomic null hypothesis by quantifying the gene regulatory activity of evolutionarily naive DNA, using RNA-seq of evolutionarily distant DNA expressed in yeast and computational predictions of random DNA activity in human cells and tissues. In yeast, we found that >99% of bases in naive DNA expressed as part of one or more transcripts. Naive transcripts are sometimes spliced, and are similar to evolved transcripts in length and expression distribution, indicating that stable expression and/or splicing are insufficient to indicate adaptation. However, naive transcripts do not achieve the extreme high expression levels as achieved by evolved genes, and frequently overlap with antisense transcription, suggesting that selection has shaped the yeast transcriptome to achieve high expression and coherent gene structures. In humans, we found that, while random DNA is predicted to have minimal activity, dinucleotide content-matched randomized DNA is predicted to have much of the regulatory activity of evolved sequences, including active chromatin marks at between half (DNase I and H3K4me3) and 1/16th (H3K27ac and H3K4me1) the rate of evolved DNA, and the repression-associated H3K27me3 at about twice the rate of evolved DNA. Naive human DNA is predicted to be more cell type-specific than evolved DNA and is predicted to generate co-occurring chromatin marks, indicating that these are not reliable indicators of selection. However, extreme high activity is rarely achieved by naive DNA, consistent with these arising via selection. Our results indicate that evolving regulatory activity from naive DNA is comparatively easy in both yeast and humans, and we expect to see many biochemically active and cell type-specific DNA sequences in the absence of selection. Such naive biochemically active sequences have the potential to evolve a function or, if sufficiently detrimental, selection may act to repress them.

genomics↗

GIL: A Python package for designing custom indexing primers

Next-generation sequencing allows samples to be multiplexed by adding a unique DNA index to each sample. Multiplexing greatly reduces the price of sequencing large numbers of samples, yet the minimum cost per sample remains high when using commercially available indexing kits and designing custom indexes is challenging. To address these issues, we created GIL (Generate Indexes for Libraries), a software tool that designs indexing primers for producing multiplexed sequencing libraries. GIL can be customized in numerous ways to meet user specifications, including index length, sequencing modality, color balancing, and compatibility with existing primers, and produces ordering and demultiplexing-ready outputs. GIL is written in Python and is freely available on GitHub at https://github.com/de-Boer-Lab/GIL. It can also be accessed as a web-application implemented in Streamlit at https://dbl-gil.streamlitapp.com.

bioinformatics↗

Robust control of replication initiation in the absence of DnaA-ATP {leftrightharpoons} DnaA-ADP regulatory elements in Escherichia coli

Investigating a long-standing conceptual question in bacterial physiology, we examine why DnaA, the bacterial master replication initiator protein, exists in both ATP and ADP forms, despite only the ATP form being essential for initiation. We engineered the {Delta}4 Escherichia coli strain, devoid of all known external elements facilitating the DnaA-ATP/ADP conversion, and found that these cells display nearly wild-type behaviors under non-overlapping replication cycles. However, during rapid growth with overlapping cycles, {Delta}4 cells exhibit initiation instability. This aligns with our model predictions, suggesting that the intrinsic ATPase activity of DnaA alone is sufficient for robust initiation control in E. coli and the DnaA-ATP/ADP conversion regulatory elements extend the robustness to multifork replication, indicating an evolutionary adaptation. Moreover, our experiments revealed constant DnaA concentrations during steady-state cell elongation in both wild-type and {Delta}4 cells. These insights not only advance our understanding of bacterial cell-cycle regulation and DnaA, but also highlight a fundamental divergence from eukaryotic cell-cycle controls, emphasizing protein copy-number sensing in bacteria versus programmed protein concentration oscillations in eukaryotes.

microbiology↗

A pandemic clonal lineage of the wheat blast fungus

Wheat, the most important food crop, is threatened by a blast disease pandemic. Here, we show that a clonal lineage of the wheat blast fungus recently spread to Asia and Africa following two independent introductions from South America. Through a combination of genome analyses and laboratory experiments, we show that the decade-old blast pandemic lineage can be controlled by the Rmg8 disease resistance gene and is sensitive to strobilurin fungicides. However, we also highlight the potential of the pandemic clone to evolve fungicide-insensitive variants and sexually recombine with African lineages. This underscores the urgent need for genomic surveillance to track and mitigate the spread of wheat blast outside of South America, and to guide pre-emptive wheat breeding for blast resistance.

evolutionary biology↗

Identification of sex chromosomes using genomic and cytogenetic methods in a range-expanding spider, Argiope bruennichi (Araneae: Araneidae)

Differences between sexes in growth, ecology and behavior strongly shape species biology. In some animal groups, such as spiders, it is difficult or impossible to identify the sex of juveniles based on external morphology. This information would be useful for field surveys, behavioral experiments, and ecological studies on e.g. sex ratios and dispersal. In species with sex chromosomes, sex can be determined based on the specific sex chromosome complement. Additionally, information on the sequence of sex chromosomes provides the basis for studying sex chromosome evolution. We combined cytogenetic and genomic data to identify the sex chromosomes in the sexually dimorphic spider Argiope bruennichi, and designed RT-qPCR sex markers. We found that genome size and GC content of this spider falls into the range reported for the majority of araneids. The male karyotype is formed by 24 acrocentric chromosomes with an X1X20 sex chromosome system, with little similarity between X chromosomes, suggesting origin of these chromosomes by X chromosome fission or early duplication of an X chromosome and subsequent independent differentiation of the copies. Our data suggest similarly sized X chromosomes in A. bruennichi. They are smaller chromosomes of the complement. Our findings open the door to new directions in spider evolutionary and ecological research.

genetics↗

Transcriptional dynamics of methane-cycling microbiomes are linked to seasonal CH4 fluxes in two hydromorphic and organic-rich grassland soils

Soil CH4 fluxes are driven by CH4-producing and -consuming microorganisms that determine whether soils are sources or sinks of this potent greenhouse gas. Using quantitative metatranscriptomics, we linked CH4-cycling microbiomes to net surface CH4 fluxes throughout a year in two drained peatland soils differing in grassland land-use intensity and physicochemical properties. CH4 fluxes were highly dynamic; both soils were net CH4 sources in autumn and winter and sinks in spring and summer. Despite similar net CH4 emissions, methanogen and methanotroph loads, as determined by small subunit rRNA transcripts per gram soil, differed strongly between sites. In contrast, mRNA transcript abundances were similar in both soils and correlated well with CH4 fluxes. The methane monooxygenase to methanogenesis mRNA ratio was higher in spring and summer, when the soils were net CH4 sinks. CH4 uptake was linked to an increased proportion of USC and {gamma} and pmoA2 pmoA transcripts. We assume that methanogen transcript abundance may be useful to approximate changes in net surface CH4 emissions from drained peat soils; high methanotroph to methanogen ratios would indicate CH4 sink properties. Our study shows the strength of quantitative metatranscriptomics; mRNA transcript abundance holds promising indicator to link soil microbiome functions to ecosystem-level processes.

microbiology↗

Development of a Coronavirus Disease 2019 Nonhuman Primate Model Using Airborne Exposure

Airborne transmission is predicted to be a prevalent route of human exposure with SARS-CoV-2. Aside from African green monkeys, nonhuman primate models that replicate airborne transmission of SARS-CoV-2 have not been investigated. A comprehensive and comparative evaluation of COVID-19 in African green monkeys, rhesus macaques, and cynomolgus macaques following airborne exposure to SARS-CoV-2 was performed to define parameters critical to disease progression and the extent to which they correlate with human COVID-19. Respiratory abnormalities and viral shedding were noted for all animals, indicating successful infection. Cynomolgus macaques developed fever, and thrombocytopenia was measured for African green monkeys and rhesus macaques. Type II pneumocyte hyperplasia and alveolar fibrosis were more frequently observed in lung tissue from cynomolgus macaques and African green monkeys. The data indicate that, in addition to African green monkeys, macaques can be successfully infected by airborne SARS-CoV-2, providing viable macaque natural transmission models for medical countermeasure evaluation. One Sentence SummaryNonhuman primates develop COVID-19 following airborne virus exposure.

microbiology↗

Chromosome-level reference genome of the European wasp spider Argiope bruennichi: a resource for studies on range expansion and evolutionary adaptation

BackgroundArgiope bruennichi, the European wasp spider, has been studied intensively as to sexual selection, chemical communication, and the dynamics of rapid range expansion at a behavioral and genetic level. However, the lack of a reference genome has limited insights into the genetic basis for these phenomena. Therefore, we assembled a high-quality chromosome-level reference genome of the European wasp spider as a tool for more in-depth future studies. FindingsWe generated, de novo, a 1.67Gb genome assembly of A. bruennichi using 21.5X PacBio sequencing, polished with 30X Illumina paired-end sequencing data, and proximity ligation (Hi-C) based scaffolding. This resulted in an N50 scaffold size of 124Mb and an N50 contig size of 288kb. We found 98.4% of the genome to be contained in 13 scaffolds, fitting the expected number of chromosomes (n = 13). Analyses showed the presence of 91.1% of complete arthropod BUSCOs, indicating a high quality of the assembly. ConclusionsWe present the first chromosome-level genome assembly in the class Arachnida. With this genomic resource, we open the door for more precise and informative studies on evolution and adaptation in A. bruennichi, as well as on several interesting topics in Arachnids, such as the genomic architecture of traits, whole genome duplication and the genomic mechanisms behind silk and venom evolution.

genomics↗

The Sle1 Cell Wall Amidase Controls Daughter Cell Splitting, Cell Size, and β-Lactam Resistance in Community Acquired Methicillin Resistant Staphylococcus aureus USA300

Most clinically relevant methicillin resistant Staphylococcus aureus (MRSA) strains have become resistant to {beta}-lactams antibiotics through horizontal acquisition of the mecA gene encoding PBP2a, a peptidoglycan transpeptidase with low affinity for {beta}-lactams. The level of resistance conferred by mecA is, however, strain dependent and the mechanisms underlying this phenomenon remain poorly understood. We here show that {beta}-lactam resistance correlates to expression of the Sle1 cell wall amidase in the fast spreading and highly virulent community-acquired MRSA USA300 clone. Sle1 is a substrate of the ClpXP protease, and while the high Sle1 levels in cells lacking ClpXP activity confer {beta}-lactam hyper-resistance, USA300 cells lacking Sle1 are as sensitive to {beta}-lactams as cells lacking mecA. This finding prompted us to assess the cellular roles of Sle1 in more detail, and we demonstrate that high Sle1 levels accelerate the onset of daughter cells splitting and decrease cell size. Vice versa, oxacillin decreases the Sle1 level, and imposes a cell-separation defect that is antagonized by high Sle1 levels, suggesting that high Sle1 levels increase tolerance to oxacillin by promoting cell separation. In contrast, increased oxacillin sensitivity of sle1 cells appears linked to a synthetical lethal effect on septum synthesis. In conclusion, this study demonstrates that Sle1 is a key factor in resistance to {beta}-lactam antibiotics in the JE2 USA300 model strain, and that PBP2a is required for expression of Sle1 in JE2 cells exposed to oxacillin.\n\nImportanceThe bacterium Staphylococcus aureus is a major cause of human disease, and the global spread of S. aureus resistant to {beta}-lactam antibiotics (MRSA) has made treatment increasingly difficult. {beta}-lactams interfere with cross-linking of the bacterial cell wall, however, the killing mechanism of this important class of antibiotics is still not fully understood. Here we provide novel insight into this topic by showing that {beta}-lactam resistance is controlled by the Sle1 cell wall amidase in the fast spreading and highly virulent MRSA USA300 clone. We show that Sle1 high levels accelerate the onset of daughter cells splitting and decrease cell size. Vice versa, oxacillin decreases the Sle1 level, and imposes a cell-separation defect that is antagonized Sle1. The key finding that resistance to {beta}-lactams correlates positively to expression of Sle1 indicates that, in S. aureus, the detrimental effects of {beta}-lactam antibiotics are linked to inhibition of daughter cells splitting.

microbiology↗