Biology subjects

Schulz, C.

Publications and source records attributed to Schulz, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Dolichol biosynthesis in yeast traces the expanded reaction pathway of higher eukaryotes

The recent reassignment of Saccharomyces cerevisiae Dfg10 as a polyprenal reductase left two unresolved steps in yeast dolichol biosynthesis: the conversion of polyprenol to polyprenal and dolichal to dolichol. In humans, both of these steps are carried out by DHRSX, an enzyme with a unique dual specificity. We found that yeast Env9 catalyzes an NADPH-dependent reduction of dolichal to dolichol. However, in contrast to DHRSX, Env9 does not catalyze the conversion of polyprenol to polyprenal. Instead, our data indicates that this reaction is catalyzed by another yeast short chain oxidoreductase, Tda5. Thus, we provide evidence that the dual role of DHRSX in human dolichol synthesis is fulfilled by two dedicated yeast enzymes, Env9 and Tda5. Accordingly, deletion of ENV9 and TDA5 led to the accumulation of polyisoprenoid intermediates, transfer of immature lipid-linked oligosaccharides onto nascent proteins, and defective N-glycosylation. This is similar to what had been observed in DHRSX-deficient mammalian cells and yeast cells with DFG10 deleted. Furthermore, we discovered that loss of Dfg10 results in a deficiency of cell wall -mannan, revealing a critical sensitivity of yeast mannan biosynthesis to the quality of nascent N-linked glycans.

biochemistry↗

bioRxiv2025

Non-invasive vagus nerve stimulation modulates Pavlovian bias in a state-dependent manner

The vagus nerve transmits vital signals between organ systems of the body and the brain. Despite growing interest in non-invasive transcutaneous vagus nerve stimulation (tVNS) for treatments of various disorders, it is not known whether its modulatory effects on behavior are dependent on bodily states. Here, we used a single-blind randomized crossover design with two within-participant factors, stimulation (right tVNS vs. sham) and metabolic state (water vs. caloric load), to investigate 54 healthy participants (210 sessions). To evaluate state-dependent changes in reinforcement learning, we used a valenced go/no-go task. Performance on this task can be used to estimate a Pavlovian choice bias, which captures improved performance for valence-congruent actions (e.g., go to win rewards) versus valence-incongruent actions (e.g., no-go to win rewards) and has been associated with dopaminergic neurotransmission. In line with theorized state-dependency of tVNS-induced changes, we observed that tVNS decreased Pavlovian response biases (Go x Win) after the caloric load (Stimulation x Load: p =.038). Taking into account individual changes in hunger but not satiety ratings best captured behavioral modulation, indicating that this modulatory effect could be driven by motivational effects related to metabolic interoception (sensed "need"). We conclude that right tVNS decreases Pavlovian response biases if the body is in a postprandial, but not a fasting state. Since fasting and Pavlovian biases have been previously associated with elevated dopamine neurotransmission, our results call for additional research on state-dependent motivational effects of tVNS to optimize interventions.

neuroscience↗

bioRxiv2025

From stomach to striatum: Ghrelin infusions increase work for rewards

Preclinical evidence demonstrates that gut signals influence motivated behavior through the dopaminergic system. However, translational research in humans is scarce, and it is not known if surges of the stomach-derived hormone ghrelin acutely boost motivation via dopamine transmission. To close this gap, we investigated the effects of acyl ghrelin infusions (vs. saline) on instrumental work for rewards, brain responses, and dopamine transmission in healthy adults in a double-blind, randomized and placebo-controlled crossover study with [11C]raclopride PET-fMRI. In line with preclinical findings, ghrelin enhanced hunger sensations (p = .007), and effort for food and small rewards. Crucially, ghrelin enhanced functional connectivity between the hypothalamus and the striatum (NAcc: pSVC = .016), as well as within the striatum (NAcc<>Putamen: pSVC = .001), pointing to an enhanced coupling between homeostatic and motivational circuits. However, ghrelin did not alter dopamine binding potential (reflecting changes in endogenous tone), but boosted task-free phasic pulses of the NAcc BOLD signal (p = .020), which were negatively associated with binding potential (p = .034). During the task, ghrelin increased cue- (precentral gyrus: pFWE = .003) and effort-evoked brain responses (e.g., VTA/SN: psvc = .002) in accordance with increases in motivation. Together, these findings recapitulate preclinical work that ghrelin primarily boosts phasic dopamine release, reflecting enhanced incentive salience of food and smaller rewards. This highlights the potential of targeting gut-brain interactions to improve motivational symptoms, such as loss of appetite or anhedonia. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=131 SRC="FIGDIR/small/691596v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@4321e6org.highwire.dtl.DTLVardef@166bda5org.highwire.dtl.DTLVardef@2ca69dorg.highwire.dtl.DTLVardef@16e93a9_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

Loss of ABC transporters, White, Brown, and Scarlet, prevents increase in mitotic divisions of germline stem cells in response to mating in Drosophila melanogaster

The replenishment of specialized cells depends on the activity of stem cells. Recent advances in stem cell research have shown that the germline stem cells (GSCs) in Drosophila melanogaster can increase their mitotic activity in response to mating. Here, we show that this ability to respond to mating is eliminated if the males are mutant for either of the ABC transporters, White (W), Brown (Bw) or Scarlet (St), which are known for their role in eye pigmentation and amine production. However, reducing the expression of w specifically from the germline cells also caused a failure to increase GSC mitotic activity upon mating, suggesting a role of w in cellular fitness. The w gene is a common genetic background for genetic experiments and frequently used as a control. Our findings underline the importance of careful experimental design and control choice.

cell biology↗

bioRxiv2025

Decoding Helicobacter pylori Resistance: Machine Learning Enhanced Prediction of Antibiotic Susceptibility using Whole-Genome Sequencing

BackgroundHelicobacter pylori is a significant risk factor for gastric cancer, peptic ulcers, and MALT lymphoma. Rising antibiotic resistance rates complicate treatment strategies. While nucleotide sequence based assays are reliable in predicting clarithromycin and levofloxacin resistance, predicting metronidazole resistance is more challenging due to diverse metabolic pathways contributing to resistance, and high genomic variability. MethodsWe assembled a cohort of 483 H. pylori clinical isolates, combining whole-genome sequencing with phenotypic susceptibility testing. Machine learning models (SVM, XGBoost, FNN) were trained on genomic variants to predict resistance phenotypes. A sliding-window approach and SHAP-based importance scoring were used for feature selection to identify biologically relevant mutations, improving prediction accuracy, particularly for metronidazole resistance. ResultsThe best-performing FNN model improved metronidazole resistance prediction by 16% compared to conventional (non-ML, single polymorphisms) sequence-based detection methods applied to the same strain collection. Feature selection identified 32 feature sets, with 11 sets significantly improving F1-scores over the baseline. Combining 2-4 feature sets revealed 53 synergistic combinations across all models. Validation showed that 87% of these combinations significantly outperformed non-ML molecular testing, with 16 combinations achieving F1-scores above 0.65. ConclusionMachine-learning can significantly improve the performance of sequence-based susceptibility testing for metronidazole in H. pylori. Novel candidate predictive markers identified from whole-genome data offer testable hypotheses about yet unexplored mechanisms of metronidazole resistance. These findings support the potential for ML-based approaches to enable more accurate susceptibility-guided therapies.

microbiology↗

bioRxiv2025

Discovery and optimization of a guanylhydrazone-based small molecule to replace bFGF for cell culture applications

Replacing growth factors with a synthetic alternative molecule is an attractive opportunity to increase consistency, scalability and cost-effectiveness of cell-based products. Herein, we describe the discovery of a chemical class of FGFR1 agonists mimicking the action of basic fibroblast growth factor (bFGF), an essential component of cell-culture media. The guanylhydrazone-based molecule, TCB-32, was identified via structure-based virtual screening on the orthosteric binding site of FGFR1. It was shown to significantly increase cell proliferation by activating the FGFR1 signalling pathway like bFGF and exhibited enhanced thermostability over bFGF by containing activity over the course of several days. After extensive structure-activity relationship studies it was possible to increase potency and efficacy leading to three highly potent agonists. This finding has the potential to remove current bottlenecks in large-scale cell production as required for applications like cultivated meat or cell therapy. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/635029v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@1d734aaorg.highwire.dtl.DTLVardef@1c28e0corg.highwire.dtl.DTLVardef@1fbdaa2org.highwire.dtl.DTLVardef@1cedd5e_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIDiscovery of a highly potent small molecule to replace bFGF in serum-free medium C_LIO_LIActivation of proliferation through the FGFR1-signalling pathway C_LIO_LIEnhanced thermal stability over bFGF C_LIO_LISAR led to three small molecules with decreased EC50, named TCB-494, TCB-541 and TCB-621 C_LI

biochemistry↗

bioRxiv2025

The Ustilago maydis transcription factor Nit2 controls nitrate assimilation during biotrophy and adjusts organic nitrogen metabolism in maize leaves under N limitation

Little is known on how filamentous phytopathogens adapt to nitrogen limitation in the host plant. In previous work, we have shown that the transcription factor Nit2 plays a major role for the utilization of non-favored nitrogen sources like nitrate, minor amino acids or nucleobases in saprotrophic sporidia of the basidiomycete corn smut fungus Ustilago maydis. Here, we employed{Delta} nit2 mutants in the natural FB1 x FB2 background to identify Nit2 regulated genes during biotrophy and investigated the impact of Nit2 on the physiology of leaf galls in nitrogen replete versus nitrogen limited host plants. RNA-Seq analysis of galls caused by the U. maydis {Delta}nit2 mutant and by the U. maydis wild type, revealed that about one third of the genes affected by Nit2 deletion during fungal biotrophy are involved in nitrogen metabolism and transport. Induction of the nitrate assimilation cluster was completely dependent on Nit2 and under nitrogen limitation,{Delta} nit2 leaf galls accumulated nitrate and showed reduced accumulation of the nitrogen-rich phloem transport amino acids asparagine and glutamine compared to wild type galls. In nitrogen replete conditions, only asparagine content was reduced in{Delta} nit2 leaf galls compared to wild type galls. Since total protein content in galls and pathogenicity were comparable between fungal genotypes in both nitrogen regimes, our findings demonstrate that nitrate utilization is dispensable for Ustilago maydis during biotrophy and can likely be compensated by increased utilization of abundant organic nitrogen sources, like asparagine, GABA and glutamine, which occurs in a partially Nit2-dependent fashion.

plant biology↗

bioRxiv2024

The N-glycosylation defect in Lec5 and Lec9 CHO cells is caused by absence of the DHRSX gene

Glycosylation-deficient Chinese hamster ovary (CHO) cell lines have been instrumental in the discovery of N-glycosylation machinery. Yet, the molecular causes of the glycosylation defects in the Lec5 and Lec9 mutants have been elusive, even though for both cell lines a defect in dolichol formation from polyprenol was previously established. We recently found that dolichol synthesis from polyprenol occurs in three steps consisting of the conversion of polyprenol to polyprenal by DHRSX, the reduction of polyprenal to dolichal by SRD5A3 and the reduction of dolichal to dolichol, again by DHRSX. This led us to investigate defective dolichol synthesis in Lec5 and Lec9 cells. Both cell lines showed increased levels of polyprenol and its derivatives, concomitant with decreased levels of dolichol and derivatives, but no change in polyprenal levels, suggesting DHRSX deficiency. Accordingly, N-glycan synthesis and changes in polyisoprenoid levels were corrected by complementation with human DHRSX but not with SRD5A3. Furthermore, the typical polyprenol dehydrogenase and dolichal reductase activities of DHRSX were absent in membrane preparations derived from Lec5 and Lec9 cells, while the reduction of polyprenal to dolichal, catalyzed by SRD5A3, was unaffected. Long-read whole genome sequencing of Lec5 and Lec9 cells did not reveal mutations in the ORF of SRD5A3, but the genomic region containing DHRSX was absent. Lastly, we established the sequence of Chinese hamster DHRSX and validated that this protein has similar kinetic properties to the human enzyme. Our work therefore identifies the basis of the dolichol synthesis defect in CHO Lec5 and Lec9 cells.

biochemistry↗

bioRxiv2023

Innate immune memory after brain injury drives inflammatory cardiac dysfunction

The enormous medical burden of stroke is not only due to the brain injury itself and the acute systemic effects, but is largely determined by chronic comorbidities that develop secondarily after stroke. We hypothesized that the high rate of comorbidity developing after a stroke might have a shared immunological cause, however, the chronic effects of brain injury on systemic immunity have so far been barely investigated. Here, we identified myeloid innate immune memory as a cause of remote organ dysfunction after stroke. Using single-cell sequencing, we identified persistent pro-inflammatory transcriptomic changes in resident monocytes/macrophages in multiple organs one month after experimental ischemic brain injury, which was particularly abundant in the heart and associated with the development of cardiac fibrosis and diastolic dysfunction. A similar phenotype was seen in myocardial autopsy samples from stroke versus control patients. We observed chronic functional changes in myeloid hematopoiesis driven by post-stroke IL-1{beta}-mediated epigenetic changes. These alterations could be transplanted to naive recipient mice and were sufficient to induce cardiac dysfunction. By effectively blocking the trafficking of pro-inflammatory monocytes from the bone marrow to the heart using a dual CCR2/5 inhibitor, we successfully prevented post-stroke cardiac dysfunction. This approach holds promising potential as a novel immune-targeted secondary prevention therapy. We anticipate that the epigenetic immune reprogramming mechanisms detailed here for the brain-heart axis could be generalized to provide a novel framework for explaining the development of various comorbidities after acute tissue injury in remote organs.

immunology↗

bioRxiv2023

Increased pulmonary monocyte infiltration and attenuated phagocytosis defines perinatal dysfunction of innate immunity in Cystic Fibrosis

In Cystic Fibrosis (CF) patients, cycles of infection and inflammation lead to fatal lung damage. While diminished mucus clearance is restored by highly effective CFTR modulator therapy, inflammation and infection persist in treated patients, suggesting alternative mechanisms may contribute to impaired immunity in CF. Here, we made use of a CF pig model to investigate the innate immune system at birth, before the onset of infection. We observed a substantial change in the composition of tissue resident immune cells towards emergency myelopoiesis, accompanied by increased infiltration of monocytes into CF lungs. A more immature status in the transcriptome profile of classical monocytes in CF pigs and preschool children with CF correlated with reduced phagocytic capacity, confirming a congenital and translationally conserved aberration of the immune system in CF. The lack of CFTR expression in circulating monocytes indicates an indirect etiology of these effects and suggests that additional immunological treatments are necessary for CF patients. One Sentence SummaryIncreased infiltration of lung tissue by monomyeloid cells and their impaired phagocytic potential cause dysfunctional imprinting of mucosal immunity in Cystic Fibrosis airways at birth and suggest early and specific treatment of the innate immune system in patients.

immunology↗

bioRxiv2023

Vaccination with Helicobacter pylori attachment proteins protects against gastric cancer

Most cases of gastric cancer are caused by chronic Helicobacter pylori infection, but the lack of early onco-diagnostics and a high risk for antibiotic resistance hampers early intervention through eradication of H. pylori infection by antibiotics. We reported on a protective mechanism where H. pylori gastric mucosal attachment can be reduced by natural antibodies that block the binding of its attachment protein BabA. Here we show that challenge infection with H. pylori induced response of such blocking antibodies in both human volunteers and in rhesus macaques, that mucosal vaccination with BabA protein antigen induced blocking antibodies in rhesus macaques, and that vaccination in a mouse model induced blocking antibodies that reduced gastric mucosal inflammation, preserved the gastric juice acidity, and fully protected the mice from gastric cancer caused by H. pylori.

immunology↗

bioRxiv2023

Resident and recruited macrophages differentially contribute to cardiac healing after myocardial ischemia

Cardiac macrophages are heterogenous in phenotype and functions, which has been associated with differences in their ontogeny. Despite extensive research, our understanding of the precise role of different subsets of macrophages in ischemia/reperfusion injury remains incomplete. We here investigated macrophage lineages and ablated tissue macrophages in homeostasis and after I/R injury in a CSF1R-dependent manner. Genomic deletion of a fms-intronic regulatory element (FIRE) in the Csf1r locus resulted in specific absence of resident homeostatic and antigen-presenting macrophages, without affecting the recruitment of monocyte-derived macrophages to the infarcted heart. Specific absence of homeostatic, monocyte-independent macrophages altered the immune cell crosstalk in response to injury and induced proinflammatory neutrophil polarization, resulting in impaired cardiac remodelling without influencing infarct size. In contrast, continuous CSF1R inhibition led to depletion of both resident and recruited macrophage populations. This augmented adverse remodelling after I/R and led to an increased infarct size and deterioration of cardiac function. In summary, resident macrophages orchestrate inflammatory responses improving cardiac remodelling, while recruited macrophages determine infarct size after I/R injury. These findings attribute distinct beneficial effects to different macrophage populations in the context of myocardial infarction. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=88 SRC="FIGDIR/small/539799v4_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@14fa4bcorg.highwire.dtl.DTLVardef@1c86bbborg.highwire.dtl.DTLVardef@118edfcorg.highwire.dtl.DTLVardef@1b06916_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2023

A critical role of retinoic acid concentration for the induction of a fully human-like atrial phenotype in hiPSC-CM

Retinoic acid (RA) induces an atrial phenotype in human induced pluripotent stem cells (hiPSC), but expression of atrium-selective currents such as the ultrarapid (IKur) and acetylcholine-stimulated K+ current (IK,ACh) is variable and less than in adult human atrium. We suspected methodological issues and systematically investigated the concentration-dependency of RA. RA treatment increased IKur concentration-dependently from 1.1{+/-}0.54 pA/pF (0 RA) to 3.8{+/-}1.1, 5.8{+/-}2.5 and 12.2{+/-}4.3 at 0.01, 0.1 and 1 {micro}M, respectively. Only 1 {micro}M RA induced enough IKur to fully reproduce human atrial AP shape and a robust shortening of action potentials (AP) upon carbachol. We found that sterile filtration caused substantial loss of RA. We conclude that 1 {micro}M RA appears necessary and sufficient to induce a full atrial AP shape in hiPSC-CM in EHT format. RA concentrations are prone to methodological issues and may profoundly impact success of atrial differentiation.

pharmacology and toxicology↗

bioRxiv2022

How gut hormones shape reward: a systematic review of the role of ghrelin and GLP-1 in human fMRI

The gastrointestinal hormones ghrelin and glucagon-like peptide-1 (GLP-1) have opposite secretion patterns, as well as opposite effects on metabolism and food intake. Beyond their role in energy homeostasis, gastrointestinal hormones have also been suggested to modulate the reward system. However, the potential of ghrelin and GLP-1 to modulate reward responses in humans has not been systematically reviewed before. To evaluate the convergence of published results, we first conduct a multi-level kernel density meta-analysis of studies reporting a positive association of ghrelin (Ncomb= 353, 18 contrasts) and a negative association of GLP-1 (Ncomb = 258, 12 contrasts) and reward responses measured using task functional magnetic resonance imaging (fMRI). Second, we complement the meta-analysis using a systematic literature review, focusing on distinct reward phases and applications in clinical populations that may account for variability across studies. In line with preclinical research, we find that ghrelin increases reward responses across studies in key nodes of the motivational circuit, such as the nucleus accumbens, pallidum, putamen, substantia nigra, ventral tegmental area, and the dorsal mid insula. In contrast, for GLP-1, we did not find sufficient convergence in support of reduced reward responses. Instead, our systematic review identifies potential differences of GLP-1 on anticipatory versus consummatory reward responses. Based on a systematic synthesis of available findings, we conclude that there is considerable support for the neuromodulatory potential of gut-based circulating peptides on reward responses. To unlock their potential for clinical applications, future studies may move beyond anticipated rewards to cover other reward facets. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/518539v2_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@19c0b00org.highwire.dtl.DTLVardef@19630e7org.highwire.dtl.DTLVardef@16498c3org.highwire.dtl.DTLVardef@169469e_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2022

The lncRNA landscape of cardiac resident macrophages and identification of Schlafenlnc as a regulator of macrophage migratory function

Cardiac resident macrophages (crMPs) were recently shown to exert pivotal functions in cardiac homeostasis and disease, but the underlying molecular mechanisms are largely unclear. Long non-coding RNAs (lncRNAs) are increasingly recognized as important regulatory molecules in a number of cell types, but neither the identity nor the molecular mechanisms of lncRNAs in crMPs are known. Here, we have employed deep RNA-seq and single cell RNA sequencing to resolve the crMP lncRNA landscape from healthy and diseased murine myocardium. CrMPs express previously unknown and highly cell type-specific lncRNAs, among which one lncRNA, termed Schlafenlnc, was particularly abundant and enriched in crMPs. We found Schlafenlnc to be necessary for migration-associated gene expression in macrophages in vitro and in vivo and essential for their adhesion and migration. Collectively, our data provide a basis to the systematic characterization of lncRNAs in crMPs and establish Schlafenlnc as a critical regulator of macrophage migratory functions.

cell biology↗

bioRxiv2022

Integrated transcriptome analysis of Huntingtons disease iPSC-derived and mouse astrocytes implicates dysregulated synaptogenesis, actin, and astrocyte maturation

Huntingtons disease (HD) is a neurodegenerative disease caused by an expanded CAG repeat within the Huntingtin (HTT) gene having dysregulated cellular homeostasis in the central nervous system, particularly in the striatum and cortex. Astrocytes establish and maintain neuronal functions through the secretion of soluble factors and physical interactions with other neurovascular unit cell types. Under pathological conditions, astrocytes can become reactive, causing cell state transitions that affect brain function. To investigate transitions between cellular states in unaffected and HD astrocytes at high resolution, single-nuclei RNA-sequencing (snRNA-seq) was performed on human HD patient induced pluripotent stem cell (iPSC)-derived astrocytes and on striatal and cortical tissue from a rapidly progressing HD mouse model (R6/2). Analysis of HD human and mouse astrocytes revealed both models have alterations in morphology, glutamate uptake, and dysregulation of astrocyte identity and maturation, whereas dysregulated actin-mediated signaling was unique to human iPSC-derived astrocytes. Representative proteins showed altered levels by Western. In both species, HD transcriptional changes reveal potential astrocyte maturation deficits that were potentially driven by astrogliogenesis transcription factors, including ATF3 and NFIA. When perturbed in a drosophila model of HD, knockdown of NFIA in glia rescued the climbing deficit. These data further support the hypothesis that mutant HTT induces dysregulated astrocyte cell states resulting in dysfunctional astrocytic properties, suggests that some of these states are cell autonomous and maybe unique to human HD, and implicate ATF3 and maturation deficits in HD pathogenesis.

neuroscience↗

bioRxiv2022

Plasmacytoid dendritic cells regulate megakaryocyte and platelet homeostasis

Platelet homeostasis is essential for vascular integrity and immune defense. While the process of platelet formation by fragmenting megakaryocytes (thrombopoiesis) has been extensively studied, the cellular and molecular mechanisms required to constantly replenish the pool of megakaryocytes by their progenitor cells (megakaryopoiesis) remains unclear. Here we use intravital 2 photon microscopy to track individual megakaryopoiesis over days. We identify plasmacytoid dendritic cells (pDCs) as crucial bone marrow niche cells that regulate megakaryopoiesis. pDCs monitor the bone marrow for platelet-producing megakaryocytes and deliver IFN- to the megakaryocytic niche to trigger local on-demand proliferation of megakaryocyte progenitors. This fine-tuned coordination between thrombopoiesis and megakaryopoiesis is crucial for megakaryocyte and platelet homeostasis in steady state and stress. However, uncontrolled pDC function within the megakaryocytic niche is detrimental. Accordingly, we show that pDCs activated by SARS-CoV2 drive inappropriate megakaryopoiesis associated with thrombotic complications. Together, we uncover a hitherto unknown megakaryocytic bone marrow niche maintained by the constitutive delivery of pDC-derived IFN-.

immunology↗

bioRxiv2022

A study of a diauxic growth experiment using an expanded dynamic flux balance framework

Flux balance analysis (FBA) remains one of the most used methods for modeling the entirety of cellular metabolism, and a range of applications and extensions based on the FBA framework have been generated. Dynamic flux balance analysis (dFBA), the expansion of FBA into the time domain, still has issues regarding accessibility limiting its widespread adoption and application, such as a lack of a consistently rigid formalism and tools that can be applied without expert knowledge. Recent work has combined dFBA with enzyme-constrained flux balance analysis (decFBA), which has been shown to greatly improve accuracy in the comparison of computational simulations and experimental data, but such approaches generally do not take into account the fact that altering the enzyme composition of a cell is not an instantaneous process. Here, we have developed a decFBA method that explicitly takes enzyme change constraints (ecc) into account, decFBAecc. The resulting software is a simple yet flexible framework for using genome-scale metabolic modeling for simulations in the time domain that has full interoperability with COBRA toolbox 3.0. To assess the quality of the computational predictions of decFBAecc, we conducted a diauxic growth fermentation experiment with Escherichia coli BW2523 in glucose minimal M9 medium. The comparison of experimental data with dFBA, decFBA and decFBAecc predictions demonstrates how systematic analyses within a fixed constraint-based framework can aid the study of model parameters. Finally, in explaining experimentally observed phenotypes, our computational analysis also demonstrates the importance of non-linear dependence of exchange fluxes on medium metabolite concentrations and the non-instantaneous change in enzyme composition, effects of which have not previously been accounted for in constraint-based analysis.

systems biology↗