Biology subjects

Jung, M.

Publications and source records attributed to Jung, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Synthesis and Biological Evaluation of Nipecotic Acid Derivatives with Terminally Double-Substituted Allenic Spacers as mGAT4 Inhibitors

A series of nipecotic acid derivatives, featuring a four- and five-carbon atom allenic spacer connecting the nitrogen of the polar nipecotic acid head with up to two aromatic residues, has been synthesized. For the synthesis of the respective nipecotic acid derivatives displaying N-substituents consisting of carbon chains with a terminal allenic function with two, mostly aryl residues a CuI-catalyzed cross-coupling of diaryldiazomethanes or N-tosylhydrazones with nipecotic acid derived terminal alkynes served as a key step. Upon characterization of these compounds regarding their inhibitory potency at mGAT1-4 and binding affinity for mGAT1, a highly potent mGAT4 inhibitor has been identified, which is defined as nipecotic acid derivative with a four-carbon atom allenic spacer terminally carrying two 4-chlorophenyl residues. The (S)-enantiomer of this compound, (S)-1-[4,4-bis(4-chlorophenyl)buta-2,3-dien-1-yl]piperidine-3-carboxylic acid [(S)-8d, DDPM-3960], displays potencies in the higher nanomolar range at mGAT4 and its human equivalent hGAT-3 with pIC50 values of 6.59 {+/-} 0.01 and 6.49 {+/-} 0.10, respectively, which are significantly higher than that of the well-known mGAT4 inhibitor (S)-SNAP-5114. In vivo evaluation of this compound revealed its significant anticonvulsant activity in several mouse models of chemically- and electrically-induced seizures. In addition to this, anxiolytic-like properties of DDPM-3960 were shown. These beneficial biological effects observed in mice were not accompanied by any serious motor deficits, making DDPM-3960 an interesting lead structure for further development.

pharmacology and toxicology↗

bioRxiv2024

Structural Insights into Broad-Range Polyphosphate Kinase 2 II Enzymes Applicable for Pyrimidine Nucleoside Diphosphate Synthesis

Polyphosphate kinases (PPK) play crucial roles in various biological processes, including energy storage and stress responses, through their interaction with inorganic polyphosphate (polyP) and the intracellular nucleotide pool. Members of the PPK family 2 (PPK2s) catalyse polyP-consuming phosphorylation of nucleotides. In this study, we characterised two PPK2 enzymes from Bacillus cereus (BcPPK2) and Lysinibacillus fusiformis (LfPPK2) to investigate their substrate specificity and potential for selective nucleotide synthesis. Both enzymes exhibited a broad substrate scope, selectively converting over 85% of pyrimidine nucleoside monophosphates (NMPs) to nucleoside diphosphates (NDPs), while nucleoside triphosphate (NTP) formation was observed only with purine NMPs. Preparative enzymatic synthesis of cytidine diphosphate (CDP) was applied to achieve an yield of 49%. Finally, structural analysis of five crystal structures of BcPPK2 and LfPPK2 provided insights into their active sites and substrate interactions. This study highlights PPK2-II enzymes as promising biocatalysts for the efficient and selective synthesis of pyrimidine NDPs.

biochemistry↗

bioRxiv2024

Engineered paediatric tumours retain patient tumour genotype and phenotype for precision medicine.

Precision medicine for paediatric and adult cancers that includes drug sensitivity profiling, can identify effective therapies for individual patients. However, obtaining adequate biopsy samples for high-throughput (HTP) screening remains challenging, with tumours needing to be expanded in culture or patient-derived xenografts - this is time-consuming and often unsuccessful. Herein, we have developed paediatric patient-derived tumour models using an engineered extracellular matrix (ECM) tissue mimic hydrogel system and HTP 3D bioprinting. Gene expression analysis from neuroblastoma and sarcoma patients identified key components of the ECM in these tumour types. Engineered hydrogels with ECM-mimic peptides were used to create patient-specific tumour organoids, modelling tumour growth conditions. Expanded tumour organoids recapitulated the genetic and phenotypic characteristics of the original tumours and retained tumourgenicity. Screening of these models identified individualised drug sensitivities. Our approach offers a timely and clinically relevant technology platform for precision medicine in paediatric cancers, potentially transforming preclinical testing across cancer types.

cancer biology↗

bioRxiv2024

Flexible 3D kirigami probes for in vitro and in vivo neural applications

Three-dimensional (3D) microelectrode arrays (MEAs) are gaining popularity as brain-machine interfaces and platforms for studying electrophysiological activity. Interactions with neural tissue depend on the electrochemical, mechanical, and spatial features of the recording platform. While planar or protruding two-dimensional MEAs are limited in their ability to capture neural activity across layers, existing 3D platforms still require advancements in manufacturing scalability, spatial resolution, and tissue integration. In this work, we present a customizable, scalable, and straightforward approach to fabricate flexible 3D kirigami MEAs containing both surface and penetrating electrodes, designed to interact with the 3D space of neural tissue. These novel probes feature up to 512 electrodes distributed across 128 shanks in a single flexible device, with shank heights reaching up to 1 mm. We successfully deployed our 3D kirigami MEAs in several neural applications, both in vitro and in vivo, and identified spatially dependent electrophysiological activity patterns. Flexible 3D kirigami MEAs are therefore a powerful tool for large-scale electrical sampling of complex neural tissues while improving tissue integration and offering enhanced capabilities for analyzing neural disorders and disease models where high spatial resolution is required.

neuroscience↗

bioRxiv2024

Narratives for positive nature futures in Europe

O_LIThe Nature Futures Framework (NFF) is a novel tool for the development of positive scenarios centred on the relationship of nature and people, emphasising biodiversity as part of the solution to environmental challenges across various spatial and temporal scales, explicitly addressing a plurality of values for nature. C_LIO_LIIn this work, we describe the process that has led to the formulation of continental-scale positive narratives for conservation in Europe based on the NFF and its value perspectives (Nature for Nature; Nature for Society; Nature as Culture), through a stakeholder group elicitation. We focused on 6 topics in the narratives: Nature Protection and Restoration; Forestry; Freshwater Ecosystems; Urban Systems; Agriculture, and Energy. We analyse differences and similarities among the narratives across these topics. C_LIO_LIWe develop three novel Nature Futures narratives for Europe with contrasting perspectives and priorities for the six topics. Within the EU socioeconomic trends and policy framework, common solutions that simultaneously tackle biodiversity conservation and instrumental and cultural Natures Contributions to People (NCP) provision emerged. C_LIO_LIThis set of narratives may integrate preferences concerning EU-level conservation targets and plausible socio-ecological development pathways, supporting the modelling of positive scenarios for nature that can be crucial in guiding policy decisions towards recovery of nature. C_LI

ecology↗

bioRxiv2024

Evaluation of genomic and phenomic prediction for application in apple breeding

Apple breeding schemes can be improved by using genomic prediction models to forecast the performance of breeding material. These models predictive ability depends on factors like trait genetic architecture, training set size, relatedness of the selected material to the training set, and the validation method used. Alternative genotyping methods such as RADseq and complementary data from near-infrared spectroscopy could help improve the cost-effectiveness of genomic selection. However, the impact of these factors and alternative approaches on predictive ability beyond experimental populations still need to be investigated. In this study, we evaluated 137 prediction scenarios varying the described factors and alternative approaches, offering recommendations for implementing genomic selection in apple breeding. Our results show that extending the training set with germplasm related to the predicted breeding material can improve average predictive ability across eleven studied traits by up to 0.08. The study emphasizes the usefulness of leave-one-family-out validation, reflecting the application of genomic selection to a new family, although it reduced average predictive ability across traits by up to 0.24 compared to cross-validation. Similar average predictive abilities across traits indicate that imputed RADseq data could be a suitable genotyping alternative to SNP array datasets. The best-performing scenario using near-infrared spectroscopy data for phenomic prediction showed a 0.35 decrease in average predictive ability across traits compared to conventional genomic prediction, suggesting that the tested phenomic selection approach is impractical. These findings offer valuable guidance for applying genomic selection in apple breeding, ultimately leading to the development of breeding material with improved quality.

genomics↗

bioRxiv2024

Integrative multi-environmental genomic prediction in apple

Genomic prediction for multiple environments can aid the selection of genotypes suited to specific soil and climate conditions. Methodological advances allow effective integration of phenotypic, genomic (additive, non-additive), and large-scale environmental (enviromic) data into multi-environmental genomic prediction models. These models can also account for genotype-by-environment interaction, utilize alternative relationship matrices (kernels), or substitute statistical approaches with deep learning. However, the application of multi-environmental genomic prediction in apple remained limited, likely due to the challenge of building multi-environmental datasets and structurally complex models. Here, we applied efficient statistical and deep learning models for multi-environmental genomic prediction of eleven apple traits with contrasting genetic architectures by integrating genomic- and enviromic-based model components. Incorporating genotype-by-environment interaction effects into statistical models improved predictive ability by up to 0.08 for nine traits compared to the benchmark model. This outcome, based on Gaussian and Deep kernels, shows these alternatives can effectively substitute the standard G-BLUP. Including non-additive effects slightly improved predictive ability by up to 0.03 for two traits, but enviromic-based effects resulted in no improvement. The deep learning approach achieved the highest predictive ability for three traits with simpler genetic architectures, outperforming the benchmark by up to 0.10. Our results demonstrate that the tested statistical models capture genotype-by-environment interactions particularly well, and the deep learning models efficiently integrate data from diverse sources. This study will foster the adoption of multi-environmental genomic prediction to select apple cultivars adapted to diverse environmental conditions, providing an opportunity to address climate change impacts.

plant biology↗

bioRxiv2024

Characterization of Tgl2, a putative lipase in yeast mitochondria

Mitochondria derive the majority of their lipids from other organelles through contact sites. These lipids, primarily phosphoglycerolipids, are the main components of mitochondrial membranes. In the cell, neutral lipids like triacylglycerides (TAGs) are stored in lipid droplets, playing an important role in maintaining cellular health. Enzymes like lipases mobilize these TAGs according to cellular needs. Neutral lipids have not yet been reported to play an important role in mitochondria so the presence of a putative TAG lipase - Tgl2, in yeast mitochondria is surprising. Moreover, TGL2 and MCP2, a high-copy suppressor for ERMES deficient cells, display genetic interactions suggesting a potential link to lipid metabolism. In this study, we characterize in detail Tgl2. We show that Tgl2 forms dimers through intermolecular disulfide bridges and a cysteine-dependent high molecular weight complex. Furthermore, we could identify the lipase motif and catalytic triad of Tgl2 through in silico comparison with other lipases and mutated the catalytically active residues accordingly. Both mutants failed to rescue the growth phenotype of mcp2{Delta}/tgl2{Delta} double deletion strain suggesting that the residues are indeed essential for the proteins function. Additionally, we discovered that the catalytically active aspartate residue is important for protein stability. Steady state level analyses with non-functional variants of Tgl2 led to the identification of Yme1 as the protease responsible for its quality control. Finally, we provide evidence that the overall increase in TAGs in cells lacking Mcp2 and Tgl2 originates from the mitochondria. Collectively, our study provides new insights into a key player in mitochondrial lipid homeostasis.

biochemistry↗

bioRxiv2024

The conserved membrane-proximal domain of Sbh1/ Sec61β guides signal peptides into the Sec61 channel

In eukaryotes, protein secretion begins with protein translocation through the universally conserved Sec61 channel into the endoplasmic reticulum (ER). Its {beta}-subunit, Sbh1 in yeast, enhances ER import of proteins with specific suboptimal signal peptides by an unknown mechanism. The Sbh1 cytosolic N-terminus consists of an intrinsically disordered, non-conserved region (IDR) that has never been visualized in active channel structures, but is close to the translocating polypeptide in the cytosolic channel vestibule. The Sbh1/Sec61{beta} N-terminal IDR is followed by structured 15 amino acids and its C-terminal transmembrane helix, both of which are conserved. We show here that the proline and adjacent conserved residues at the Sbh1 cytosolic/transmembrane domain interface form a hinge that positions the Sbh1 cytosolic domain across the channel vestibule and orients it with respect to the lateral gate. This orientation is critical for Sbh1-dependent protein insertion into the channel. Sbh1-dependence of Sec61 channel insertion is a function of the signal peptide of the respective secretory protein. By chemical crosslinking of purified cytosolic domains of Sbh1 and its paralog Sbh2 to synthetic signal peptides derived from their respective client proteins, we show that the cytosolic domains of Sbh1 and Sbh2 contain specific signal peptide binding sites. The position of the crosslinked residues suggests that signal peptide binding is mediated by the IDRs. We conclude that Sec61{beta} homologs directly recognize signal peptides of their substrates and guide them into the Sec61 channel; they thus control entry of specific proteins into the secretory pathway.

biochemistry↗

bioRxiv2023

FGF8-mediated gene regulation affects regional identity in human cerebral organoids

The morphogen FGF8 establishes graded positional cues imparting regional cellular responses via modulation of early target genes. The roles of FGF signaling and its effector genes remain poorly characterized in human experimental models mimicking early fetal telencephalic development. We used hiPSC-derived cerebral organoids as an in vitro platform to challenge the effect of FGF8 signaling on neural identity and differentiation. We found that FGF8 treatment increases cellular heterogeneity leading to distinct telencephalic and mesencephalic-like domains that co-develop in multi-regional organoids. Within telencephalic domains, FGF8 affects the anteroposterior and dorsoventral identity of neural progenitors, the balance between GABAergic and glutamatergic neurons, thus impacting spontaneous neuronal network activity. Moreover, FGF8 efficiently modulates key regulators responsible for several human neurodevelopmental disorders. Overall, our results show that FGF8 signaling is directly involved in both regional patterning and cellular diversity in human cerebral organoids and in modulating genes associated with normal and pathological neural development.

developmental biology↗

bioRxiv2023

RNA polymerase II transcription with partially assembled TFIID complexes

The recognition of core promoter sequences by the general transcription factor TFIID is the first step in the process of RNA polymerase II (Pol II) transcription initiation. Metazoan holo-TFIID is composed of the TATA binding protein (TBP) and of 13 TBP associated factors (TAFs). Inducible Taf7 knock out (KO) results in the formation of a Taf7-less TFIID complex, while Taf10 KO leads to serious defects within the TFIID assembly pathway. Either TAF7 or TAF10 depletions correlate with the detected TAF occupancy changes at promoters, and with the distinct phenotype severities observed in mouse embryonic stem cells or mouse embryos. Surprisingly however, under either Taf7 or Taf10 deletion conditions, TBP is still associated to the chromatin, and no major changes are observed in nascent Pol II transcription. Thus, partially assembled TFIID complexes can sustain Pol II transcription initiation, but cannot replace holo-TFIID over several cell divisions and/or development.

molecular biology↗

bioRxiv2023

Inhibition of the macrophage demethylase LSD1 reverses Leishmania amazonensis-induced transcriptomic changes and causes a decrease in parasite load

Intracellular pathogens exploit host cell functions to favor their own survival. In recent years, the subversion of epigenetic regulation has emerged as a key microbial strategy to modify host cell gene expression and evade antimicrobial immune responses. Using the protozoan parasite Leishmania as a model system, we have recently demonstrated that infection causes histone H3 hypomethylation, which is associated with the establishment of an anti-inflammatory phenotype, suggesting that host cell demethylases may play a role in the intracellular survival of these parasites. In this study, we combined pharmacological inhibition with RNA sequencing and quantitative immune-precipitation analysis to investigate the role of the macrophage lysine demethylase LSD1 (KDM1a) in Leishmania intracellular infection in vitro. Treatment of infected macrophages with validated, LSD1-specific inhibitors resulted in a significant reduction in parasite burden. We confirmed the impact of these inhibitors on LSD1 activity within macrophage nuclear extracts using an in vitro demethylase assay and established their LSD1 target engagement in situ by cellular thermal shift assay. RNA-seq analysis of infected and inhibitor-treated macrophages linked parasite killing to a partial reversion of infection-dependent expression changes, restoring the macrophage anti-microbial response and limiting cholesterol biosynthesis. While we ruled out any impact of Leishmania on LSD1 expression or localization, we uncovered significant alterations in LSD1 complex formation within infected macrophages, involving unique interactions with host cell regulatory proteins such as Rcor-1. Our study sheds important new light on the epigenetic mechanisms of macrophage immuno-metabolic subversion by intracellular Leishmania and identifies LSD1 as a potential candidate for host-directed, anti-leishmanial therapy.

cell biology↗

bioRxiv2023

The genetic basis of apple shape and size unraveled by digital phenotyping

Great diversity of shape, size, and skin color is observed among the fruits of different apple genotypes. These traits are critical for consumers and therefore interesting targets for breeding new apple varieties. However, they are difficult to phenotype and their genetic basis, especially for fruit shape and ground color, is largely unknown. We used the fruit FruitPhenoBox to digitally phenotype 506 genotypes of the apple reference population (apple REFPOP) genotyped for 303,148 single nucleotide polymorphism (SNP) markers. From the apple images, 573 highly heritable features describing fruit shape and size as well as 17 highly heritable features for fruit skin color were extracted to explore genotype-phenotype relationships. Out of these features, nine and four principal components (PCs) as well as 16 and eight uncorrelated features were chosen to carry out genome-wide association studies for fruit shape, size, and fruit skin color, respectively. In total, 69 SNPs scattered over all 17 apple chromosomes were significantly associated with round, conical, cylindrical, or symmetric fruit shapes and fruit size. Novel associations with major effect on round or conical fruit shapes and fruit size were identified on chromosomes 1 and 2. Additionally, 16 SNPs associated with PCs and uncorrelated features related to red over color as well as green and yellow ground color were found on eight chromosomes. The identified associations can be used to advance marker-assisted selection in apple fruit breeding to systematically select for desired fruit appearance.

plant biology↗

bioRxiv2023

A novel PEX14/PEX5 interface links peroxisomal protein import and receptor recycling

Newly synthesized peroxisomal proteins are recognized in the cytosol by the cycling receptor PEX5 and directed to a docking complex comprising PEX14 and PEX13 at the peroxisomal membrane. After cargo translocation, the unloaded PEX5 is recycled in an ATP-dependent manner. Receptor docking involves the WxxxF-motifs in the N-terminal domain (NTD) of PEX5 that are recognized by the N-terminal domain of PEX14. Here, we combine biochemical methods and NMR spectroscopy to identify a novel binding interface between human PEX5 and PEX14. The interaction involves the PEX5 C-terminal cargo-binding TPR domain and a conserved IPSWQI peptide motif in the C-terminal intrinsically disordered region of PEX14. The three-dimensional structure of the PEX14 IPSWQI peptide bound the PEX5 TPR domain, shows the PEX14 interaction is non-overlapping with PTS1 binding to the TPR domain. Notably, PEX14 IPSWQI motif binding to a hinge region in the TPR domain shows a more open supercoil of the TPR fold that resembles the apo conformation in the absence of PTS1 peptide. Mutation of binding site residues in PEX5 or PEX14 leads to a partial protein import defect and decrease of the steady-state-concentration of PEX5. This resembles the mutant phenotype of cells affected in receptor recycling, suggesting a role in this process.

biochemistry↗

bioRxiv2023

Structure of recombinant formate dehydrogenase from Methylobacterium extorquens (MeFDH1)

Formate dehydrogenase (FDH) is critical for the conversion between formate and carbon dioxide. Despite its importance, the structural complexity of FDH and difficulties in the production of the enzyme have made it difficult to elucidate its unique physicochemical properties. Here, we purified recombinant Methylobacterium extorquens AM1 FDH (MeFDH1) and used cryo-electron microscopy to determine its structure. We resolved a heterodimeric MeFDH1 structure at a resolution of 2.8 [A], showing a noncanonical active site and a well-embedded Fe-S redox chain relay. In particular, the tungsten bis-molybdopterin guanine dinucleotide active site showed an open configuration with the flexible C-terminal cap domain, suggesting structural and dynamic heterogeneity in the enzyme. SIGNIFICANCE- A recombinant MeFDH1 from an inducible expression system - Structural characterization of recombinant MeFDH1 for its catalytic activity - A dynamic, open configuration of the C-terminal cap domain

biophysics↗

bioRxiv2023

Modelling the probability of meeting IUCN Red List criteria to support reassessments.

Comparative extinction risk analysis - which predicts species extinction risk from correlation with traits or geographical characteristics - has gained research attention as a promising tool to support extinction risk assessment in the IUCN Red List of Threatened Species. However, its uptake has been very limited so far, possibly because these models only predict a species Red List category, without indicating which Red List criteria may be triggered by which such approaches cannot easily be used in Red List assessments. We overcome this implementation gap by developing models that predict the probability of species meeting individual Red List criteria. Using data on the worlds birds, we evaluated the predictive performance of our criterion-specific models and compared it with the typical criterion-blind modelling approach. We compiled data on biological traits (e.g., range size, clutch size) and external drivers (e.g., change in canopy cover) often associated with extinction risk. For each specific criterion, we modelled the relationship between extinction risk predictors and species Red List category under that criterion using ordinal regression models. We found criterion-specific models were better at predicting threatened species compared to a criterion-blind model (higher sensitivity), but less good at predicting not threatened species (lower specificity). As expected, different covariates were important for predicting threat status under different criteria, for example change in annual temperature was important to predict criteria related to population trends, while clutch size was important for criteria related to restricted area of occupancy or small population size. Our criteria-specific method can support Red List assessors by producing outputs that identify species likely to meet specific criteria, and which are the most important predictors: these species can be prioritised for re-evaluation. We expect this new approach to increase the uptake of extinction risk models in Red List assessments, bridging a long-standing research-implementation gap.

ecology↗

bioRxiv2023

Serine synthesis pathway upregulated by E-cadherin is essential for the proliferation and metastasis of breast cancers

The loss of E-cadherin (E-cad), an epithelial cell adhesion molecule, has been implicated in the epithelial-mesenchymal transition (EMT), promoting invasion and migration of cancer cells and, consequently, metastasis. However, recent studies have demonstrated that E-cad supports the survival and proliferation of metastatic cancer cells, suggesting that our understanding of E-cad in metastasis is far from comprehensive. Here, we report that E-cad upregulates the de novo serine synthesis pathway (SSP) in breast cancer cells. The SSP provides metabolic precursors for biosynthesis and resistance to oxidative stress, critically beneficial for E-cad-positive breast cancer cells to achieve faster tumor growth and more metastases. Inhibition of PHGDH, a rate-limiting enzyme in the SSP, significantly and specifically hampered the proliferation of E-cad-positive breast cancer cells and rendered them vulnerable to oxidative stress, inhibiting their metastatic potential. Our findings reveal that E-cad adhesion molecule significantly reprograms cellular metabolism, promoting tumor growth and metastasis of breast cancers.

cancer biology↗

bioRxiv2023

The Mechanical Influence of Densification on Initial Epithelial Architecture

Epithelial tissues are the most abundant tissue type in animals, lining body cavities and generating compartment barriers. The function of a monolayer epithelium - whether protective, secretory, absorptive, or filtrative -relies on regular tissue architecture with respect to the apical-basal axis. Using an unbiased 3D analysis pipeline developed in our lab, we previously showed that epithelial tissue architectures in culture can be divided into distinct developmental categories, and that these are intimately connected to cell density: at sparse densities, cultured epithelial cell layers have a squamous morphology (Immature); at intermediate densities, these layers develop lateral cell-cell borders and rounded cell apices (Intermediate); cells at the highest densities reach their full height and demonstrate flattened apices (Mature). These observations prompted us to ask whether epithelial architecture emerges from the mechanical constraints of densification, and to what extent a hallmark feature of epithelial cells, namely cell-cell adhesion, contributes. In other words, to what extent is the shape of cells in an epithelial layer a simple matter of sticky, deformable objects squeezing together? We addressed this problem using a combination of computational modeling and experimental manipulations. Our results show that the first morphological transition, from Immature to Intermediate, can be explained simply by cell crowding. Additionally, we identify a new division (and thus transition) within the Intermediate category, and find that this second morphology relies on cell-cell adhesion.

cell biology↗