Biology subjects

Dietrich, V.

Publications and source records attributed to Dietrich, V..

5 recordsLinked to original sources

bioRxiv2024

Direct RNA sequencing (RNA004) allows for improved transcriptome assessment and near real-time tracking of methylation for medical applications

Direct RNA sequencing (DRS) is a nanopore-based technique for analyzing RNA in its native form, promising breakthroughs in diagnostics and biomarker development. Coupled to RNA002 sequencing chemistry, its clinical implementation has been challenging due to low throughput, low accuracy, and lack of large-scale RNA-modification models. In this study, we evaluate the improvements achieved by pairing the latest RNA004 chemistry with novel modified-base-calling models for pseudouridine and N6-methyladenosine using diverse RNA samples from cell lines, synthetic oligos, and human blood. Finally, we present the first clinical application of DRS by confirming the loss of RNA methylation in a patient carrying truncating mutations in the methyltransferase METTL5. Conclusively, the combined use of RNA004 chemistry with the base-calling models significantly improved the throughput, accuracy, and site-specific detection of modifications. From this perspective, we offer an outlook on the potential suitability of DRS for use in routine diagnostics, the first comprehensive benchmark of human peripheral blood and quality assessments of RNA therapeutics.

bioinformatics↗

bioRxiv2023

Plasmodesmata act as unconventional membrane contact sites regulating inter-cellular molecular exchange in plants

Membrane contact sites (MCS) are fundamental for intracellular communication, but their role in intercellular communication remains unexplored. We show that in plants, plasmodesmata communication bridges function as atypical endoplasmic reticulum (ER)-plasma membrane (PM) tubular MCS, operating at cell-cell interfaces. Similar to other MCS, ER-PM apposition is controlled by a protein-lipid tethering complex, but uniquely, this serves intercellular communication. Combining high-resolution microscopy, molecular dynamics, pharmacological and genetic approaches, we show that cell-cell trafficking is modulated through the combined action of Multiple C2 domains and transmembrane domain proteins (MCTP) 3, 4, and 6 ER-PM tethers, and phosphatidylinositol-4-phosphate (PI4P) lipid. Graded PI4P amounts regulate MCTP docking to the PM, their plasmodesmata localization and cell-cell permeability. SAC7, an ER-localized PI4P-phosphatase, regulates MCTP4 accumulation at plasmodesmata and modulates cell-cell trafficking capacity in a cell-type specific manner. Our findings expand MCSs functions in information transmission, from intracellular to intercellular cellular activities. In briefPlant intercellular communication is regulated via tubular membrane contact through PI4P binding-ER-PM tether MCTP proteins HighlightsO_LIPlasmodesmata are unconventional ER/PM tubular contact sites located at cell-cell interface C_LIO_LIPlasmodesmata operate as control valves, modulating ER-PM contacts to regulate transport C_LIO_LIMCTP3, MCTP4, MCTP6 and PI4P tethering elements act as valve regulators C_LIO_LISAC7 PI4P phosphatase controls plasmodesmata MCS in a cell-type-specific manner C_LI

plant biology↗

bioRxiv2023

Genome-wide DNA methylation changes in human spermatogenesis

Sperm production and function require the correct establishment of DNA methylation patterns in the germline. Here, we examined the genome-wide DNA methylation changes during human spermatogenesis and its alterations in disturbed spermatogenesis. We found that spermatogenesis is associated with remodeling of the methylome, comprising a global-decline in DNA methylation in primary spermatocytes followed by selective remethylation, resulting in a spermatid-specific methylome. Hypomethylated regions in spermatids were enriched in specific transcription factor binding sites for DMRT and SOX family members and spermatid-specific genes. Intriguingly, while SINEs displayed differential methylation throughout spermatogenesis, LINEs appeared to be protected from changes in DNA methylation. In disturbed spermatogenesis, germ cells exhibited considerable DNA methylation changes, which were significantly enriched at transposable elements and genes involved in spermatogenesis. We detected hypomethylation in SVA and L1HS in disturbed spermatogenesis, suggesting an association between the abnormal programming of these regions and failure of germ cells progressing beyond meiosis.

genetics↗

bioRxiv2020

In silico design of Phl p 6 variants with altered folding stability significantly impacts antigen processing, immunogenicity and immune polarization

AbstactO_ST_ABSIntroductionC_ST_ABSProtein fold stability has been proposed to represent an intrinsic feature contributing to immunogenicity and immune polarization by influencing the amount of peptide-MHC II complexes (pMHCII). Using in silico prediction, we introduced point mutations in proteins that either increase or decrease their fold-stability without altering immunodominant epitopes or changing the overall structure of the protein. Here, we investigated how modulation of the fold-stability of the grass pollen allergen Phl p 6 affects its ability to stimulate immune responses and T cell polarization. MethodsUsing the MAESTRO software tool, stabilizing or destabilizing mutations were selected and verified by molecular dynamics simulations. The mutants were expressed in E. coli, purified tag-free, and analyzed for thermal stability and resistance to endolysosomal proteases. The resulting peptides were analysed by degradome assay and mass spectrometry. The structure of the most stable mutant protein was obtained by X-ray crystallography. We evaluated the capacity of the mutants to stimulate T cell proliferation in vitro, as well as antibody responses and T cell polarization in vivo in an adjuvant-free BALB/c mouse model. ResultsFour stabilizing and two destabilizing mutations were identified by MAESTRO. Experimentally determined changes in thermal stability compared to the wild type protein ranged from -5 to +14 {degrees}C. Destabilization led to faster proteolytic processing in vitro, whereas highly stabilized mutants were degraded very slowly. However, the overall pattern of identified peptides remained very similar. This was confirmed in bone marrow derived dendritic cells that processed and presented the immune dominant epitope from a destabilized mutant more efficiently. In vivo, stabilization resulted in a shift in immune polarization as indicated by higher levels of IgG2a and increased secretion of TH1/TH17 cytokines. ConclusionMAESTRO was very efficient in detecting single point mutations that increase or reduce fold-stability. Thermal stability correlated well with susceptibility to protease resistance and presentation of pMHCII on the surface of dendritic cells in vitro. This change in processing kinetics significantly influenced the polarization of T cell responses in vivo. Modulating the fold-stability of proteins thus has the potential to optimize and polarize immune responses, which opens the door to more efficient design of molecular vaccines.

immunology↗

bioRxiv2018

Weight statistics controls dynamics in recurrent neural networks

Recurrent neural networks are complex non-linear systems, capable of ongoing activity in the absence of driving inputs. The dynamical properties of these systems, in particular their long-time attractor states, are determined on the microscopic level by the connection strengths wij between the individual neurons. However, little is known to which extent network dynamics is tunable on a more coarse-grained level by the statistical features of the weight matrix. In this work, we investigate the dynamical impact of three statistical parameters: density (the fraction of non-zero connections), balance (the ratio of excitatory to inhibitory connections), and symmetry (the fraction of neuron pairs with wij = wji). By computing a phase diagram of network dynamics, we find that balance is the essential control parameter: Its gradual increase from negative to positive values drives the system from oscillatory behavior into a chaotic regime, and eventually into stationary fix points. Only directly at the border of the chaotic regime do the neural networks display rich but regular dynamics, thus enabling actual information processing. These results suggest that the brain, too, is fine-tuned to the edge of chaos by assuring a proper balance between excitatory and inhibitory neural connections.\n\nAuthor summaryComputations in the brain need to be both reproducible and sensitive to changing input from the environment. It has been shown that recurrent neural networks can meet these simultaneous requirements only in a particular dynamical regime, called the edge of chaos in non-linear systems theory. Here, we demonstrate that recurrent neural networks can be easily tuned to this critical regime of optimal information processing by assuring a proper ratio of excitatory and inhibitory connections between the neurons. This result is in line with several micro-anatomical studies of the cortex, which frequently confirm that the excitatory-inhibitory balance is strictly conserved in the cortex. Furthermore, it turns out that neural dynamics is largely independent from the total density of connections, a feature that explains how the brain remains functional during periods of growth or decay. Finally, we find that the existence of too many symmetric connections is detrimental for the above mentioned critical dynamical regime, but maybe in turn useful for pattern completion tasks.

neuroscience↗