Biology subjects

Jung, J.

Publications and source records attributed to Jung, J..

At least 73 records · Page 4Linked to original sources

bioRxiv2025

Early-life infection with Cryptosporidium parvum induces inflammatory responses to dietary antigens

To examine the effect of early-life infection with Cryptosporidium parvum on the development of oral tolerance, we developed a low-dose infection model in neonatal mice. C. parvum infection in neonatal mice results in immunopathology in the colon. IL-1{beta} released during C. parvum infection blocked the formation of colonic goblet cell associated antigen passages, which normally serve as a conduit for antigen uptake and development of peripheral regulatory T cells (pTregs), responsible for long-term oral tolerance. Following infection with C. parvum, adoptively transferred OT-II cells, which respond to ovalbumin (ova), developed reduced frequency of Foxp3+Ror{gamma}t+ cells in mesenteric lymph nodes with an expansion of TH1-like Tregs in the colon. The altered pTreg profile was accompanied by a strong TH1 immune response and robust IgG2c antibody responses to orally administered ova. Our findings suggest that intestinal inflammation and altered pTreg development leads to loss of oral tolerance during early life infection with C. parvum.

microbiology↗

bioRxiv2025

The distortion-push mechanism for the γ-subunit rotation in F1-ATPase

F1-ATPase comprises the stator ring consisting of {beta} subunits and the rotor {gamma} subunit. The {gamma} subunit rotation mechanism has been extensively investigated by biochemical analyses, structural studies, single-molecule measurements, and computational studies. Recent cryo-electron microscopy (cryo-EM) structures of F1-ATPase from the thermophilic bacterium Bacillus PS3 (TF1) provide us with further possibilities for a better understanding of the {gamma}-rotation mechanisms. Using cryo-EM structures having the {gamma}-rotation angles close to the binding dwell and catalytic dwell states, we investigate the relationships between the {gamma} subunit rotation, conformational changes of the stator 3{beta}3 subunits, and the nucleotide-binding and release. We performed targeted molecular dynamics (MD) simulations with external forces on the {beta} subunits and observed 80{degrees} substep rotations of the {gamma} subunit. Then, we optimized the most probable transition pathway through the mean-force string method simulations with 64 images. Finally, using umbrella sampling, we calculated the potential of mean forces along the minimum free energy pathway during the 80{degrees} substep rotation. Our MD simulations suggest that 80{degrees} substep rotation is divided into the first rotation, resting, and the second rotation. Notably, the first rotation is driven by the distortion of the stator 3{beta}3 subunits, and the second rotation is induced mainly by direct {beta}/{gamma} subunit interactions. This model, which we call the distortion-push mechanism, is consistent with the residue-level experimental analysis on F1-ATPase and the atomic structures determined by X-ray crystallography and cryo-EM.

biophysics↗

bioRxiv2025

Self-organized and self-sustained ensemble activity patterns in simulation of mouse primary motor cortex

The idea of self-organized signal processing in the cerebral cortex has become a focus of research since Beggs and Plentz 1 reported avalanches in local field potential recordings from organotypic cultures and acute slices of rat somatosensory cortex. How the cortex intrinsically organizes signals remains unknown. A current hypothesis was proposed by the condensed matter physicists Bak, Tang, and Wiesenfeld 2 when they conjectured that if neuronal avalanche activity followed inverse power law distributions, then brain activity may be set around phase transitions within self-organized signals. We asked if we would observe self-organized signals in an isolated slice of our data driven detailed simulation of the mouse primary motor cortex? If we did, would we observe avalanches with power-law distributions in size and duration and what would they look like? Our results demonstrate that a brief unstructured stimulus (100ms, 57A current) to a small subset of neurons (about 181 of more than 10,000) in a simulated mouse primary motor cortex slice results in self-organized and self-sustained avalanches with power-law size and duration distributions and values similar to those reported from in vivo and in vitro experiments. We observed 4 cross-layer and cross-neuron population patterns, 3 of which displayed a dominant rhythmic component. Avalanches were each composed of one or more of the 4 population patterns.

neuroscience↗

bioRxiv2024

Intraflagellar Transport Selectivity Occurs with the Proximal Portion of the Trypanosome Flagellum

Intraflagellar transport (IFT) trains move bidirectionally along the doublet microtubules (DMTs) of the axoneme within the flagellum. In Trypanosoma brucei, IFT trains predominantly associate with four of the nine DMTs. Using high-resolution microscopy, we reveal how this selective association is put in place. IFT proteins form a ring surrounding the 9 DMTs on top of the transition fibres. Volume electron microscopy revealed densities along all DMTs in the proximal portion of the flagellum, exhibiting thinner, shorter profiles with branches absent in mature IFT trains. As the axoneme extends within the flagellar pocket, IFT trains are detected but are often positioned outside DMTs 3-4/7-8. After the axoneme exits the flagellar pocket, IFT trains localise exclusively to DMTs 3-4 and 7-8. Super-resolution and expansion microscopy demonstrated that IFT proteins follow the same distribution as the IFT-like densities. This suggests they represent IFT trains undergoing assembly and/or disassembly and reveals their unexpected ability to shift from one DMT to another. SummaryIn Trypanosoma brucei, intraflagellar transport (IFT) trains selectively associate with specific axonemal microtubules. Using advanced microscopy, this study reveals how this restriction occurs at the proximal portion of the flagellum during the assembly and/or disassembly of IFT trains.

cell biology↗

bioRxiv2024

ColBuilder: Flexible structure generation of crosslinked collagen fibrils

Collagen fibrils are fundamental building blocks of connective tissues, yet generating accurate molecular models of their structure remains challenging due to their hierarchical organization and complex crosslinking patterns. ColBuilder has been developed to automate the generation of atomistic models of crosslinked collagen fibrils and facilitate the setup of molecular simulations. The tool integrates homology modeling, higher-order structure generation and optimization to build complete fibril structures with precise control over sequence composition, crosslinking patterns, and dimensions. Users can explore different collagen sequences, manipulate crosslink chemistry through mixed ratios and densities, and generate fibrils of varying diameter and length. All-atom molecular dynamics simulations of 335 nm-long fibrils validate the generated structures, showing excellent agreement with experimental measurements of D-band periodicity and force-extension behavior. ColBuilder is available both as an open-source command-line application and through a web interface at colbuilder.mpip-mainz.mpg.de.

biophysics↗

bioRxiv2024

Are resting-state networks the brain's cognitive atoms? Differential dynamic reconfiguration of functional brain networks across tasks and at rest

It is increasingly popular to utilise functional connectivity (FC) analyses of resting-state functional magnetic resonance imaging (fMRI) to characterize human functional brain networks and to use the emergent resting-state networks (RSNs) in basic and clinical neuroscience. Often, they are treated as atomic building blocks that underpin human cognition. However, the true function of these RSNs, as well as the relationship between intrinsic and task-evoked functional brain networks, are complex and incompletely characterized. Here, we investigated the functional characteristics of the intrinsic and extrinsic networks using resting-state and task fMRI. Independent component analysis (ICA) was used to estimate spatiotemporal functional networks during tasks and at rest, and to compare the spatiotemporal properties of each network. While there was some spatial correspondence between the RSNs and task-evoked networks, our results demonstrated that the task-evoked functional networks were different from the RSNs in task-relatedness as well as spatial topology. Furthermore, the degree of topological differences between the RSNs and task-evoked networks was modulated by a given task. Comparison between the RSNs and task-evoked networks showed that tasks reconfigure the RSNs by changing FC with various brain regions specific to the task condition. Our findings indicate that the brain does not maintain an "invariant intrinsic" network architecture when it engages in a task. Instead, the tasks reconfigure the network architectures, thereby accommodating specific computational/representational task requirements through flexible interactions between demand-specific regions. Thus, the results suggest that task fMRI is required to understand the full repertoire of the brains functional architecture. Significant StatementResting-state networks (RSNs) could offer a critical foundation for understanding the brains intrinsic organization. However, the functional nature of these intrinsic networks, and their relationship to those activated during specific tasks, are complex and not fully understood. We undertook a comprehensive examination of the functional attributes of intrinsic and extrinsic networks. Although we observed some spatial congruence between RSNs and task-evoked networks, we found fundamental differences in their task-relatedness and spatial topology. These findings highlight the dynamic nature of the brains functional networks, which adapt to specific task demands through flexible interactions among task-specific regions. Thus, task fMRI is essential for a comprehensive understanding of how the human brain dynamically reconfigures its functional architecture in response to external demands, providing valuable insights into the cognition and behaviour.

neuroscience↗

bioRxiv2024

Structuring Role of Tau-Tubulin Co-Condensates in Early Microtubule Organization

Tau protein, a key microtubule-associated protein in neurons, is traditionally known for stabilizing microtubules. However, its recently discovered ability to undergo liquid-liquid phase separation (LLPS) reveals a broader, dynamic role in nucleating and organizing microtubule networks. Here, using a combination of real-time imaging and a geometric approach based on Voronoi tessellation, we examined how tau condensation leads to clustering and local tubulin enrichment, supporting microtubule organization. Our observations show that tau-tubulin co-condensates not only initiate nucleation and branching of microtubules but also drive the networks gradual evolution through a "dynamic weaving" process. By generating Voronoi diagrams from super-resolution and confocal microscopy images of the stabilized network, we quantitatively mapped tubulin enrichment as a function of tau density, revealing that high-density tau clusters, approximately 0.2 m in size, correlate with tubulin-rich spots at equilibrium. Overall, these findings provide new insights into tau-tubulin co-condensates as dynamic structuring elements, whose liquid-like properties continuously reshape the microtubule network, creating a flexible and adaptive architecture essential for cellular function.

biophysics↗

bioRxiv2024

In silico nanoscope to study the interplay of genome organization and transcription regulation

In eukaryotic genomes, regulated access and communication between cis-regulatory elements (CREs) are necessary for enhancer-mediated transcription of genes. The molecular framework of the chromatin organization underlying such communication remains poorly understood. To better understand it, we develop a multiscale modeling pipeline to build near-atomistic models of the 200 kb Nanog gene locus in mouse embryonic stem cells comprising nucleosomes, transcription factors, co-activators, and RNA polymerase II-Mediator complexes. By integrating diverse experimental data, including protein localization, genomic interaction frequencies, cryo-electron microscopy, and single-molecule fluorescence studies, our model offers novel insights into chromatin organization and its role in enhancer-promoter communication. The models equilibrated by high-performance molecular dynamics simulations span a scale of [~]350 nm, revealing an experimentally consistent local and global organization of chromatin and transcriptional machinery. Our models elucidate that the sequence-regulated chromatin accessibility facilitates the recruitment of transcription regulatory proteins exclusively at CREs, guided by the contrasting nucleosome organization compared to other regions. By constructing an experimentally consistent near-atomic model of chromatin in the cellular environment, our approach provides a robust framework for future studies on nuclear compartmentalization, chromatin organization, and transcription regulation.

molecular biology↗

bioRxiv2024

Fast Single-Cell MALDI Imaging of Low-Mass Metabolites Reveals Cellular Activation Markers

Single-cell MALDI mass spectrometry imaging (MSI) of lipids and metabolites >200 Da has recently come to the forefront of biomedical research and chemical biology, but fast metabolome-preserving methods without paraformaldehyde fixation for analysis of low mass, hydrophilic metabolites (<200 Da) in large cell populations are lacking. Introducing giant unilamellar vesicles (GUVs) as MSI ground truth for cell-sized objects and Monte Carlo reference-based consensus clustering for data-dependent identification of cell subpopulations. The PRISM-MS (PRescan Imaging for Small Molecule - Mass Spectrometry) dual-scan MSI workflow is presented, enabling space-efficient and therefore faster lipid analysis in single GUVs and cells. Beyond lipids, PRISM-MS enables MSI and on-cell MS2-based identification of low-mass metabolites like amino acids or Krebs cycle intermediates involved in stimulus-dependent cell activation. The utility of PRISM-MS is demonstrated through the characterization of complex metabolome changes in lipopolysaccharide (LPS)-stimulated microglial cells and human-induced pluripotent stem cell-derived microglia. Translation of single cell results to endogenous microglia in organotypic hippocampal slice cultures indicates that LPS-activation involves changes of the itaconate-to-taurine ratio and alterations in neuron-to-glia glutamine-glutamate shuttling. The data suggests that PRISM-MS could serve as a standard method in single cell metabolomics, given its capability to characterize larger cell populations and low-mass metabolites.

bioinformatics↗

bioRxiv2024

A brain-shuttled antibody targeting alpha synuclein aggregates for the treatment of synucleinopathies

Parkinsons disease and multiple system atrophy are members of a class of devastating neurodegenerative diseases called synucleinopathies, which are characterized by the presence of alpha-synuclein (-Syn) rich aggregates in the brains of patients. Passive immunotherapy targeting these aggregates is an attractive disease-modifying strategy. Such an approach must not only demonstrate target selectivity towards -Syn aggregates, but also achieve appropriate brain exposure to have the desired therapeutic effect. Here we present preclinical data for a next-generation antibody for the treatment of synucleinopathies. SAR446159 (ABL301) is a bispecific antibody composed of an -Syn-binding immunoglobulin (IgG) and an engineered insulin-like growth factor receptor 1 (IGF1R) binding single-chain variable fragment (scFv), acting as a shuttle to transport an antibody across the blood-brain barrier (BBB). SAR446159 binds tightly and preferentially to -Syn aggregates and prevents their seeding capacity in vitro and in vivo. Incubation with SAR446159 reduced -Syn preformed fibrils (PFFs) uptake in neurons and facilitated uptake and clearance by microglia. In wild type mice injected in the striatum with -Syn PFFs, treatment with SAR446159 reduced the spread of aSyn pathology as measured by phosphorylated -Syn staining and lessened the severity of motor phenotypes. Additionally, in 9-month-old transgenic mice overexpressing -Syn (mThy1--Syn, Line 61), repeated treatment with SAR446159 reduced markers of -Syn aggregation in the brain. SAR446159 had significantly higher brain and CSF penetration over a sustained period than its monospecific counterpart (1E4) in rats and monkeys. The binding properties of SAR446159 combined with its brain-shuttle technology make it a potent, next-generation immunotherapeutic for treating synucleinopathies.

neuroscience↗

bioRxiv2024

De novo design of α-helical peptide channels with designer stoichiometry

Despite advances in peptide and protein design, the rational design of membrane-spanning peptides that form conducting channels remains challenging due to our imperfect understanding of the sequence-to-structure relationships that drive membrane insertion, assembly, and conductance. Here, we describe the design and computational and experimental characterization of a series of coiled coil-based peptides that form transmembrane -helical barrels. Through a combination of rational and computational design, we obtain barrels with 5 to 7 helices, as characterized in detergent micelles. In lipid bilayers, these peptide assemblies exhibit two conductance states with relative populations dependent on the applied potential: (i) a low-conductance states that correlate with variations in the modeled coiled-coil barrel geometries, indicating stable transmembrane -helical barrels; and (ii) high-conductance states in which single pores change size in discrete steps. Notably, the high-conductance states are similar for all peptides in contrast to the low-conductance states. This indicates the formation of large, dynamic pores through the recruitment and expulsion of peptides, as observed in natural barrel-stave peptide pores. These findings establish rational routes to design and tune functional membrane-spanning peptide channels with specific conductance and geometry.

synthetic biology↗

bioRxiv2024

Tau condensation on DNA and localization on centromeres: A potential link to cell division

Tau protein, traditionally recognized for stabilizing microtubules and forming pathological aggregates, has recently been observed to form condensates in various contexts. While its condensation with RNA has been well studied, the interaction between tau and DNA, along with its biological significance, remains less explored. Here, using single-molecule experiments, we found that tau binds stably to naked DNA at nanomolar concentrations, leading to the local co- condensation of tau and DNA. These tau condensates on DNA can also interface with microtubules, leveraging taus known role in promoting microtubule growth and organization. The dynamic nature of these condensates facilitates the remodeling of the DNA-microtubule assembly. Interestingly, two phosphomimetic tau mutants, T231D/S235D and S262D, retained their affinity for DNA but differed in their ability to link microtubules to DNA. Furthermore, imaging of HEK-293 and SH-SY5Y cells in early mitosis revealed that tau localizes on centromeres, poised to capture nascent mitotic spindles. Building on these observations, we speculate that tau may play a novel role in mitosis, where tau clusters facilitate the early registration of mitotic spindles to chromosomes before kinetochore-mediated attachment. We also discuss the potential implications of this model in conditions where abnormal cell cycle re-entry and tau activity may disrupt cell division.

biophysics↗

bioRxiv2024

The role of vibration amplitude in the escape hatching response of red-eyed treefrog embryos

The function and adaptive significance of defensive behaviors depend on the contexts in which they naturally occur. Amplitude properties of predator cues are widely used by prey to assess predation risk, yet rarely studied in the context of the stimuli relevant to defensive decisions in nature. Red-eyed treefrog embryos, Agalychnis callidryas, hatch precociously in response to attacks on their arboreal egg clutches by snakes and wasps. They use vibrations excited during attacks to detect predators, but wind and rainstorms also excite intense vibrations. Past work has demonstrated that to avoid costly decision errors, A. callidryas non-redundantly combine information from the temporal and frequency properties of clutch vibrations. Here we demonstrate that embryos also use absolute amplitude and fine-scale amplitude modulation information to refine their hatching decision. We used vibration recordings to characterize the amplitude properties of the most common predator and benign-source disturbances to A. callidryas egg clutches in nature and tested whether embryos at three ages across the onset of mechanosensory-cued hatching (4-6 days) respond to amplitude variation during playback of synthetic vibrations to eggs. Older embryos responded to much lower-amplitude vibrations, reflecting a >88-fold decrease in response threshold from 4 to 5 days. To assess how embryos combine amplitude with other vibration properties, we played embryos recorded exemplars of snake attack and rain vibrations of varying amplitudes and patterns of amplitude modulation. The amplitude response curve was steeper for snake recordings than for rain. While amplitude information alone is insufficient to discriminate predator attack from benign-source vibrations, A. callidryas employ an impressively complex strategy combining absolute amplitude, amplitude modulation, temporal, and frequency information for their hatching decision.

developmental biology↗

bioRxiv2024

Developmental transcriptomics in Pristionchus reveals the logic of a plasticity gene regulatory network

Developmental plasticity enables the production of alternative phenotypes in response to different environmental conditions. While significant advances in understanding the ecological and evolutionary implications of plasticity have been made, understanding its genetic basis has lagged. However, a decade of genetic screens in the model nematode Pristionchus pacificus has culminated in 30 genes which affect mouth-form plasticity. We also recently reported the critical window of environmental sensitivity, and therefore have clear expectations for when differential gene expression should matter. Here, we collated previous data into a gene-regulatory network (GRN), and performed developmental transcriptomics across different environmental conditions, genetic backgrounds, and mouth-form mutants to assess the regulatory logic of plasticity. We found that only two genes in the GRN (eud-1 and seud-1/sult-1) are sensitive to the environment during the critical window. Interestingly, the time points of their sensitivity differ, suggesting that they act as sequential checkpoints. We also observed temporal constraint upon the transcriptional effects of mutating the GRN and revealed unexpected feedback between mouth-form genes. Surprisingly, expression of seud-1/sult-1, but not eud-1, correlated with mouth form biases across different strains and species. Finally, a comprehensive analysis of all samples identified metabolism as a shared pathway for regulating mouth-form plasticity. These data are presented in a Shiny app to facilitate gene-expression comparisons across development in up to 14 different conditions. Collectively, our results suggest that mouth-form plasticity evolved a constrained, two-tiered logic to integrate environmental information leading up to the final developmental decision.

genetics↗

bioRxiv2024

Ventricle stimulation as a potential gold-standard control stimulation site for transcranial focused ultrasound stimulation

This research investigates whether ventricular-focused ultrasound stimulation (ventricle-FUS) can serve as an effective control in studies using transcranial FUS, a non-invasive technology for brain modulation. FUS has notable potential for therapeutic applications but requires a robust control to accurately assess its effects. We evaluated the effectiveness of ventricle-FUS, as an active, non-cerebrum control for FUS research, comparing it to sham stimulation. We conducted a comprehensive assessment of ventricle-FUS, employing both questionnaires and multiple neuroimaging metrics such as grey matter and white matter volumes, and functional connectivity. Ventricle-FUS did not alter any of these metrics, thereby successfully retaining the auditory, somatosensory, and experiential elements of FUS without affecting brain structure or function. Importantly, participants were unable to distinguish whether they received ventricle-FUS or sham FUS. Our findings confirm that ventricle-FUS establishes it as a reliable control approach in FUS research, crucial for advancing its therapeutic applications.

neuroscience↗

bioRxiv2023

Parkinson's disease-related Miro1 mutation induces mitochondrial dysfunction and loss of dopaminergic neurons in vitro and in vivo

The complex and heterogeneous nature of Parkinsons disease (PD) is still not fully understood, however, increasing evidence supports mitochondrial impairments as a major driver of neurodegeneration in PD. Recently, the regulator of mitochondrial homeostasis Miro1 has been linked genetically and pathophysiologically to PD. Using 2D and 3D patient-based induced pluripotent stem cells models, including an isogenic control, showed that the Miro1 p.R272Q mutation leads to mitochondrial impairments including increased oxidative stress, disrupted mitochondrial bioenergetics and altered metabolism. This was accompanied by increased -synuclein levels in 2D dopaminergic neurons and by a significant reduction of dopaminergic neurons within midbrain organoids. Knock-in mice expressing mutant p.R285Q Miro1 (orthologue of the human p.R272Q mutation) confirmed the PD-specific dopaminergic neuronal loss in the substantia nigra, accumulation of striatal phosphorylated -synuclein accompanied by behavioral alterations. These findings demonstrate that mutant Miro1 is sufficient to comprehensively model PD-relevant phenotypes in vitro and in vivo, reinforcing its pivotal role in PD pathogenesis.

neuroscience↗

bioRxiv2023

Short-term Pre-operative Methionine Restriction Induces Browning of Perivascular Adipose Tissue and Improves Vein Graft Remodeling in Mice

Short-term preoperative methionine restriction (MetR) shows promise as a translatable strategy to modulate the bodys response to surgical injury. Its application, however, to improve post-interventional vascular remodeling remains underexplored. Here, we find that MetR protects from arterial intimal hyperplasia in a focal stenosis model and adverse vascular remodeling after vein graft surgery. RNA sequencing reveals that MetR enhances the brown adipose tissue phenotype in arterial perivascular adipose tissue (PVAT) and induces it in venous PVAT. Specifically, PPAR- was highly upregulated in PVAT-adipocytes. Furthermore, MetR dampens the post-operative pro-inflammatory response to surgery in PVAT-macrophages in vivo and in vitro. This study shows for the first time that the detrimental effects of dysfunctional PVAT on vascular remodeling can be reversed by MetR, and identifies pathways involved in browning of PVAT. Furthermore, we demonstrate the potential of short-term pre-operative MetR as a simple intervention to ameliorate vascular remodeling after vascular surgery. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/565269v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@112f51aorg.highwire.dtl.DTLVardef@1998bd8org.highwire.dtl.DTLVardef@1ac5046org.highwire.dtl.DTLVardef@1ca4c87_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2023

Tumor-wide RNA splicing aberrations generate immunogenic public neoantigens

T-cell-mediated immunotherapies are limited by the extent to which cancer-specific antigens are homogenously expressed throughout a tumor. We reasoned that recurrent splicing aberrations in cancer represent a potential source of tumor-wide and public neoantigens, and to test this possibility, we developed a novel pipeline for identifying neojunctions expressed uniformly within a tumor across diverse cancer types. Our analyses revealed multiple neojunctions that recur across patients and either exhibited intratumor heterogeneity or, in some cases, were tumor-wide. We identified CD8+ T-cell clones specific for neoantigens derived from tumor-wide and conserved neojunctions in GNAS and RPL22, respectively. TCR-engineered CD8+ T-cells targeting these mutations conferred neoantigen-specific tumor cell eradication. Furthermore, we revealed that cancer-specific dysregulation in splicing factor expression leads to recurrent neojunction expression. Together, these data reveal that a subset of neojunctions are both intratumorally conserved and public, providing the molecular basis for novel T-cell-based immunotherapies that address intratumoral heterogeneity.

cancer biology↗