Biology subjects

Jensen, T.

Publications and source records attributed to Jensen, T..

12 recordsLinked to original sources

bioRxiv2026

5-MOP: a novel and selective colony stimulating factor-1 receptor (CSF1R) radiotracer

Colony stimulating factor 1 receptor (CSF1R) is a tyrosine kinase receptor that is expressed exclusively in microglia within the CNS. Its endogenous ligands, colony stimulating factor-1 (CSF1) and interleukin-34 (IL-34), are released from neurons, positioning CSF1R as a key mediator receptor of neuron-glia communication. CSF1R is considered not only a potential drug target, but also a biomarker of neuroinflammation. From that perspective, selective radioligands for neuroimaging are of great interest for imaging neuroinflammation and determining drug occupancy. In this study, we have validated the binding characteristics of a CSF1R inhibitor, 4-((5-MethOxy-6-((5-methoxypyridin-2-yl)methoxy)pyridin-3-yl)methyl)-2-(1-methyl-1H-pyrazol-4-yl)pyrimidine (5-MOP) as a novel CSF1R radioligand, by performing in vitro saturation binding experiments in human and murine tissues. 5-MOP was found to be selective for CSF1R among a broad range of kinases. Autoradiography revealed that [3H]5-MOP binds with high affinity (KD = 9.8 nM) to a single saturable binding site in human meningioma tissues, and this binding was displaced with known CSF1R inhibitors, including CPPC, sCSF1inh and GW-2580. In contrast, CPPC, which has been extensively used as a CSF1R radioligand showed substantial cross-reactivity to other brain kinases, including Trk A/B/C, and [3H]CPPC could only be displaced with CPPC itself, not by other ligands, including 5-MOP. These results identify [3H]5-MOP as the most selective radioligand currently available, enabling accurate detection of drug occupancy and activated microglia. Significance of the studyThis study identifies and validates a novel selective radioligand that binds CSF1R with high selectivity and low nanomolar affinity. Because CSF1R is selectively expressed in activated microglia, this radioligand could be useful for detecting neuroinflammatory activity.

neuroscience↗

bioRxiv2026

Impaired renal base excretion in secretin receptor knock-out mice during prolonged base-loading

AimSecretin was recently found to play a pivotal role in the renal adaptation to acute base excess. Here, secretin increases pendrin-dependent HCO3- secretion from the beta-intercalated cells in the cortical collecting ducts. Whether secretin and its receptor play a role during prolonged base-loading remains unknown. MethodsUrine and blood acid-base analyses were carried out in secretin receptor (SCTR) KO and WT mice at baseline and after 1 and up to 8 days of base-loading with NaHCO3-enriched drinking water. Changes in pendrin protein abundance and function were assessed by immunoblotting and isolated tubule perfusion experiments. Plasma secretin levels and renal SCTR expression were assessed after 24 hours of acid/base-loading by radioimmunoassay and qPCR, respectively. ResultsSCTR KO mice responded with diminished urine alkalization and a lesser reduction of urinary acid excretion when base-loaded for 48 hours. Concordantly, SCTR KO mice presented with increased blood base retention compared with WTs. Base-loaded SCTR WT and KO mice showed comparable total pendrin protein abundance. Despite this, pendrin function was markedly lower in SCTR KO mice. Base-loaded mice had higher plasma secretin and renal SCTR levels compared with acid-loaded mice. Higher arterial HCO - associated with higher renal SCTR mRNA expression. ConclusionLoss of the SCTR diminishes renal base excretion capacity and exacerbates systemic base accumulation during prolonged base-loading. Further, plasma secretin and renal SCTR mRNA levels are modulated by acid-base intake. These findings further support a central role of secretin and its receptor in the regulation of both acute and prolonged base excess. Key pointsO_LIIn mice, the receptor of the gut hormone secretin is required for the kidney to adequately handle a sustained base load. In mice with secretin receptor knockout, renal base excretion is impaired and metabolic alkalosis is aggravated and slower to resolve. C_LIO_LIBase-loaded knockout mice up-regulate pendrin protein abundance normally, the bicarbonate-secreting Cl-/HCO3-exchanger in collecting-duct {beta}-intercalated cells, but exhibit lower pendrin function. This suggests that the defect lies in the activation of pendrin, rather than in the regulation of its abundance. C_LIO_LIRenal secretin-receptor expression increases with higher arterial bicarbonate and plasma secretin, and renal secretin receptor expression, levels are lower in acid-loaded mice compared to base-loaded mice. This indicates that the secretin/secretin receptor system is itself affected by acid-base status/acid-base intake. C_LI

physiology↗

bioRxiv2024

Recovery of highly contiguous genomes from complex terrestrial habitats reveals over 15,000 novel prokaryotic species and expands characterization of soil and sediment microbial communities

Genomes are fundamental to understanding microbial ecology and evolution. The emergence of high-throughput, long-read DNA sequencing has enabled recovery of microbial genomes from environmental samples at scale. However, expanding the microbial genome catalogue of soils and sediments has been challenging due to the enormous complexity of these environments. Here, we performed deep, long-read Nanopore sequencing of 154 soil and sediment samples collected across Denmark and through an optimised bioinformatics pipeline, we recovered genomes of 15,314 novel microbial species, including 4,757 high-quality genomes. The recovered microbial genomes span 1,086 novel genera and provide the first high-quality reference genomes for 612 previously known genera, expanding the phylogenetic diversity of the prokaryotic tree of life by 8 %. The long-read assemblies also enabled the recovery of thousands of complete rRNA operons, biosynthetic gene clusters and CRISPR-Cas systems, all of which were underrepresented and highly fragmented in previous terrestrial genome catalogues. Furthermore, the incorporation of the recovered MAGs into public genome databases significantly improved species-level classification rates for soil and sediment metagenomic datasets, thereby enhancing terrestrial microbiome characterization. With this study, we demonstrate that long-read sequencing and optimised bioinformatics, allows cost-effective recovery of high-quality microbial genomes from highly complex ecosystems, which remain the largest untapped source of biodiversity for expanding genome databases and filling in the gaps of the tree of life.

bioinformatics↗

bioRxiv2024

Structural basis for the synergistic assembly of the snRNA export complex

The nuclear cap-binding complex (CBC) and its partner ARS2 play crucial roles in regulating Pol II transcript fate through mutually exclusive interactions with RNA effectors. One such effector, PHAX, mediates the nuclear export of U-rich small nuclear RNAs (snRNAs). Here we present the cryo-EM structure of the snRNA export complex comprising phosphorylated PHAX, CBC, CRM1, Ran-GTP and capped RNA. The central region of PHAX bridges the CBC-bound capped RNA to the CRM1-RanGTP, while also significantly reinforcing cap dinucleotide binding. Additionally, PHAX interacts with a distant region of CRM1 facilitating contacts of an essential phosphorylated region with the prominent basic surface of RanGTP. The importance of these interactions is confirmed by in vitro and in cell mutagenesis experiments. CBC engagement within the snRNA export complex is incompatible with its interactions with other RNA effectors such as ALYREF or NCBP3. Taken together, we demonstrate that snRNA export complex formation requires synergistic binding of all its components, which in turn displaces ARS2 from the CBC, and commits the complex for export.

molecular biology↗

bioRxiv2024

MicroRNAs and PFAS: A Pilot Study in Blood Collected from Firefighters

Per- and polyfluoroalkyl substances (PFAS) are chemicals with widespread industrial and consumer applications, and firefighters are known to be at risk of elevated PFAS exposure due to their occupational activities. This study aims to assess PFAS exposure and explore potential mechanistic insights through miRNA sequencing of plasma exosomes, in relation to PFAS levels in the general population. The study included 34 firefighter participants. PFAS levels in plasma were analyzed, and miRNA sequencing of plasma exosomes was conducted. The findings were compared with the general population data from the National Health and Nutrition Examination Survey (NHANES). While total PFAS levels did not significantly differ between firefighters and the general population in the cohort considered, variations in individual PFAS compounds were observed. MiRNA sequencing revealed substantial heterogeneity in miRNA expression patterns. Associations between serum PFAS levels and biochemical indicators suggested potential health implications, although further mechanistic insights need to be explored.

pharmacology and toxicology↗

bioRxiv2023

Epiphytic and endophytic microbiome of the seagrass Zostera marina: Do they contribute to pathogen reduction in seawater?

Seagrass ecosystems provide crucial ecosystem services for coastal environments and were shown to reduce the abundance of pathogens linked to infections in humans and marine organisms. Among several potential drivers, seagrass phenolics released into seawater have been suggested to play role in pathogen suppression, but the potential involvement of the seagrass microbiome in such effect has not been studied. Here we hypothesized that the microbiome of the eelgrass Zostera marina, especially the leaf epiphytes that are at direct interface between the seagrass host and surrounding seawater, inhibit such pathogenic microorganisms, hence, contribute to their suppression. Using a culture-dependent approach, we isolated 88 bacteria and fungi associated with the surfaces and inner tissues of the eelgrass leaves (healthy and decaying) and the roots, plus 19 strains from surrounding seawater and sediment. We first assessed the broad-spectrum antibiotic activity of microbial extracts against a large panel of common aquatic, human (fecal) and plant pathogens, and finally mined the metabolome of 88 most active extracts. The healthy leaf epibiotic bacteria, particularly Streptomyces sp. strain 131, displayed broad-spectrum and potent antibiotic activity superior to some control drugs. Gram-negative bacteria abundant on healthy leaf surfaces, and few endosphere-associated bacteria and fungi also showed remarkable antimicrobial activity. UPLC-MS/MS-based massive untargeted metabolomics analyses showed the rich specialized metabolite repertoire of strains with low annotation rates, indicating the presence of many undescribed antimicrobials in the extracts. This study contributes to our current understanding on microbial and chemical ecology of seagrasses, implying potential involvement of the seagrass microbiome, especially the leaf epiphytes, in reduction of pathogen load in seawater. Such antibiotic activity is not only beneficial for the health of ocean, human and aquaculture sector, especially in the context of climate change that is expected to exacerbate all infectious diseases, but may also assist seagrass conservation and management strategies.

ecology↗

bioRxiv2022

Microtubule-mediated GLUT4 trafficking is disrupted in insulin resistant skeletal muscle

Microtubules serve as tracks for long-range intracellular trafficking of glucose transporter 4 (GLUT4), but the role of this process in skeletal muscle and insulin resistance is unclear. Here, we used fixed and live-cell imaging to study microtubule-based GLUT4 trafficking in human and mouse muscle fibers and L6 rat muscle cells. We found GLUT4 localized along and on the microtubules in mouse and human muscle fibers. Pharmacological microtubule disruption using Nocodazole (Noco) prevented long-range GLUT4 trafficking and depleted GLUT4-enriched structures at microtubule nucleation sites in a fully reversible manner. Using a perfused muscle-on-a-chip system to enable real-time glucose uptake measurements in isolated mouse skeletal muscle fibers, we observed that Noco maximally disrupted the microtubule network after 5 min without affecting insulin-stimulated glucose uptake. In contrast, a 2h Noco treatment markedly decreased insulin responsiveness of glucose uptake. Insulin resistance in mouse muscle fibers induced either in vitro by C2 ceramides or in vivo by diet-induced obesity, impaired microtubule-based GLUT4 trafficking. In L6 muscle cells, pharmacological activation of the microtubule motor protein kinesin-1 increased basal and insulin-stimulated GLUT4 translocation, whereas shRNA-mediated knockdown of the kinesin-1 protein encoding gene Kif5B reduced insulin-stimulated GLUT4 translocation. Thus, in adult skeletal muscle fibers, the microtubule network is essential for intramyocellular GLUT4 movement, likely functioning to maintain an insulin-responsive cell-surface recruitable GLUT4 pool via kinesin-1 mediated trafficking.

cell biology↗

bioRxiv2021

A comparative baseline of coral disease across the central Red Sea

The Red Sea is a unique environment for corals with a strong environmental gradient characterized by temperature extremes and high salinities, but minimal terrestrial runoff or riverine input and their associated pollution. Disease surveys were conducted along 22 reefs in the central Red Sea along the Saudi Arabian coast in October 2015, which coincided with a bleaching event. Our objectives were to 1) document types, prevalence, and distribution of coral diseases in a region with minimal terrestrial input, 2) compare regional differences in diseases and bleaching along a latitudinal gradient of environmental conditions, and 3) use histopathology to characterize disease lesions at the cellular level. Coral reefs of the central Red Sea had a widespread but a surprisingly low prevalence of disease (<0.5%), based on the examination of >75,750 colonies. Twenty diseases were recorded affecting 16 coral taxa and included black band disease, white syndromes, endolithic hypermycosis, skeletal eroding band, growth anomalies and focal bleached patches. The three most common diseases were Acropora white syndrome (59.1% of the survey sites), Porites growth anomalies (40.9%), and Porites white syndrome (31.8%). Over half of the coral genera within transects had lesions and corals from the genera Acropora, Millepora and Lobophyllia were the most commonly affected. Cell-associated microbial aggregates were found in four coral genera resembling patterns found in the Indo-Pacific. Differences in disease prevalence, coral cover, amount of heat stress as measured by degree heating weeks (DHW) and extent of bleaching was evident among sites. Disease prevalence was not explained by coral cover or DHW, and a negative relationship between coral bleaching and disease prevalence was found. The northern-most sites off the coast of Yanbu had the highest average DHW values but absence of bleaching and the highest average disease prevalence was recorded. Our study provides a foundation and baseline data for coral disease prevalence in the Red Sea, which is projected to increase as a consequence of increased frequency and severity of ocean warming.

ecology↗

bioRxiv2019

Physical fitness in community dwelling older adults is linked to dietary intake, gut microbiota and metabolomic signatures

When humans age, changes in body composition arise along with lifestyle-associated disorders influencing fitness and physical decline. Here we provide a comprehensive view of dietary intake, physical activity, gut microbiota (GM) and host metabolome in relation to physical fitness of 207 community dwelling subjects aged +65 years. Stratification on anthropometric/body-composition/physical-performance measurements (ABPm) variables identified two phenotypes (high/low-fitness) clearly linked to dietary intake, physical activity, GM and host metabolome patterns. Strikingly, despite a higher energy intake high-fitness subjects were characterized by leaner bodies and lower fasting proinsulin-C-peptide/blood glucose levels in a mechanism likely driven by higher dietary-fiber intake, physical activity and increased abundance of Bifidobacteriales and Clostridiales species in GM and associated metabolites (i.e. enterolactone). These factors explained 50.1% of the individual variation in physical fitness. We propose that targeting dietary strategies for modulation of GM and host metabolome interactions may allow establishing therapeutic approaches to delay and possibly revert comorbidities of aging.

cell biology↗

bioRxiv2019

The SAMPL6 SAMPLing challenge: Assessing the reliability and efficiency of binding free energy calculations

Approaches for computing small molecule binding free energies based on molecular simulations are now regularly being employed by academic and industry practitioners to study receptor-ligand systems and prioritize the synthesis of small molecules for ligand design. Given the variety of methods and implementations available, it is natural to ask how the convergence rates and final predictions of these methods compare. In this study, we describe the concept and results for the SAMPL6 SAMPLing challenge, the first challenge from the SAMPL series focusing on the assessment of convergence properties and reproducibility of binding free energy methodologies. We provided parameter files, partial charges, and multiple initial geometries for two octa-acid (OA) and one cucurbit[8]uril (CB8) host-guest systems. Participants submitted binding free energy predictions as a function of the number of force and energy evaluations for seven different alchemical and physical-pathway (i.e., potential of mean force and weighted ensemble of trajectories) methodologies implemented with the GROMACS, AMBER, NAMD, or OpenMM simulation engines. To rank the methods, we developed an efficiency statistic based on bias and variance of the free energy estimates. For the two small OA binders, the free energy estimates computed with alchemical and potential of mean force approaches show relatively similar variance and bias as a function of the number of energy/force evaluations, with the attach-pull-release (APR), GROMACS expanded ensemble, and NAMD double decoupling submissions obtaining the greatest efficiency. The differences between the methods increase when analyzing the CB8-quinine system, where both the guest size and correlation times for system dynamics are greater. For this system, nonequilibrium switching (GROMACS/NS-DS/SB) obtained the overall highest efficiency. Surprisingly, the results suggest that specifying force field parameters and partial charges is insufficient to generally ensure reproducibility, and we observe differences between seemingly converged predictions ranging approximately from 0.3 to 1.0 kcal/mol, even with almost identical simulations parameters and system setup (e.g., Lennard-Jones cutoff, ionic composition). Further work will be required to completely identify the exact source of these discrepancies. Among the conclusions emerging from the data, we found that Hamiltonian replica exchange--while displaying very small variance--can be affected by a slowly-decaying bias that depends on the initial population of the replicas, that bidirectional estimators are significantly more efficient than unidirectional estimators for nonequilibrium free energy calculations for systems considered, and that the Berendsen barostat introduces non-negligible artifacts in expanded ensemble simulations.

biophysics↗

bioRxiv2019

NADPH-oxidase 2 is required for molecular adaptations to high-intensity interval training in skeletal muscle.

Objective: Reactive oxygen species (ROS) have been proposed as signaling molecules mediating exercise training adaptation, but the ROS source has remained unclear. This study aimed to investigate the requirement for NADPH oxidase (NOX)2-dependent redox changes induced by acute and long-term high-intensity interval training (HIIT) in skeletal muscle in a mouse model lacking functional NOX2 complex due to deficient p47phox (Ncf1) subunit expression (ncf1* mutation). Methods: HIIT was investigated after an acute bout of exercise and after a chronic intervention (3x week for 6 weeks) in wildtype (WT) vs. NOX2 activity-deficient (ncf1*) mice. NOX2 activation during HIIT was measured using a genetically-encoded biosensor. Immunoblotting and single-fiber staining were performed to measure classical exercise-training responsive endpoints in skeletal muscle. Results: A single bout of HIIT increased NOX2 activity measured using electroporated p47roGFP oxidation immediately after exercise but not 1h after exercise. After a 6-week of HIIT regime, improvements in maximal running capacity and some muscle training-markers responded less to HIIT in the ncf1* mice compared to WT, including superoxide dismutase (SOD)2, catalase, hexokinase II (HK II), pyruvate dehydrogenase (PDH) and protein markers of mitochondrial oxidative phosphorylation complexes. Strikingly, HIIT-training increased mitochondrial network area and decreased fragmentation in WT mice only. Conclusion: This study provided evidence that HIIT exercise activates NOX2 complex in skeletal muscle and that the presence of functional NOX2 is required for specific skeletal muscle adaptations to HIIT relating to antioxidant defense, glucose metabolism, and mitochondria.

physiology↗

bioRxiv2017

Uncharacterized bacterial structures revealed by electron cryotomography

SUMMARY STATEMENTHere we present a survey of previously uncharacterized structures we have observed in bacterial cells by electron cryotomography, in the hopes of spurring their identification and study.\n\nABSTRACTElectron cryotomography (ECT) can reveal the native structure and arrangement of macromolecular complexes inside intact cells. This technique has greatly advanced our understanding of the ultrastructure of bacterial cells. Rather than undifferentiated bags of enzymes, we now view bacteria as structurally complex assemblies of macromolecular machines. To date, our group has applied ECT to nearly 90 different bacterial species, collecting more than 15,000 cryotomograms. In addition to known structures, we have observed several, to our knowledge, uncharacterized features in these tomograms. Some are completely novel structures; others expand the features or species range of known structure types. Here we present a survey of these uncharacterized bacterial structures in the hopes of accelerating their identification and study, and furthering our understanding of the structural complexity of bacterial cells.

microbiology↗