Biology subjects

Sigmund, F.

Publications and source records attributed to Sigmund, F..

3 recordsLinked to original sources

bioRxiv2025

Cortex-Wide Preservation of Multi-Stimulus Information across Degrees of Network Synchronization

Sensory-evoked cortical responses vary with global network dynamics, yet the link between cortical state and stimulus processing remains unclear. Here, we introduce a paradigm that jointly decodes stimulus identity and network state from wide-field calcium imaging in mice undergoing multisensory and optogenetic stimulation across isoflurane-induced transitions from compartmentalized to synchronized activity. Effective dimensionality, a summary measure of network complexity, correlated well with anesthesia depth, while non-linear contrastive learning achieved >97% stimulus decoding accuracy across all states. Individual cortical regions maintained [≥]82.5% accuracy even during deep anesthesia with prominent slow waves. Preservation of stimulus-specific information extended throughout the cortex, demonstrating that distinct representations remain decodable within synchronized networks. Direct optogenetic cortical stimulation exhibited state-invariant decoding performance, contrasting with anesthesia-dependent decline observed for sensory stimuli. Multi-stimulus cortical representations remain decodable across varying levels of network synchronization, with implications for brain-machine interfaces and clinical tools that assess preserved cortical responsiveness under variable arousal conditions.

neuroscience↗

bioRxiv2019

Iron-sequestering nanocompartments as multiplexed Electron Microscopy gene reporters

Multi-colored gene reporters such as fluorescent proteins are indispensable for biomedical research, but equivalent tools for electron microscopy (EM), a gold standard for deciphering mechanistic details of cellular processes1,2 and uncovering the network architecture of cell-circuits3,4, are still sparse and not easily multiplexable. Semi-genetic EM reporters are based on the precipitation of exogenous chemicals5-9 which may limit spatial precision and tissue penetration and can affect ultrastructure due to fixation and permeabilization. The latter technical constraints also affect EM immunolabeling techniques10-13 which may furthermore be complicated by limited epitope accessibility. The fully genetic iron storage protein ferritin generates contrast via its electron-dense iron core14-16, but its small size complicates differentiation of individual ferritin particles from cellular structures. To enable multiplexed gene reporter imaging via conventional transmission electron microscopy (TEM), we here introduce the encapsulin system of Quasibacillus thermotolerans (Qt) as a fully genetic iron-biomineralizing nanocompartment. We reveal by cryo-electron reconstructions that the Qt monomers (QtEnc) self-assemble to nanospheres with T=4 icosahedral symmetry and an ~44 nm diameter harboring two putative pore regions at the fivefold and threefold axes. We furthermore show that the native cargo (QtlMEF) auto-targets to the inner surface of QtEnc and exhibits ferroxidase activity leading to efficient iron sequestration inside mammalian cells. We then demonstrate that QtEnc can be robustly differentiated from the non-intermixing encapsulin of Myxococcus xanthus17 (Mx, ~32 nm) via a deep-learning model, thus enabling automated multiplexed EM gene reporter imaging in mammalian cells.

synthetic biology↗

bioRxiv2017

Eukaryotically expressed encapsulins as orthogonal compartments for multiscale molecular imaging

We have genetically controlled compartmentalization in eukaryotic cells by heterologous expression of bacterial encapsulin shell and cargo proteins to engineer enclosed enzymatic reactions and size-controlled metal biomineralization. The orthogonal shell protein (EncA) from M. xanthus efficiently auto-assembled inside mammalian cells into nanocompartments to which sets of native (EncB,C,D) and engineered cargo proteins self-targeted. This enabled localized bimolecular fluorescence and enzyme complementation with selective access to substrates via the pores in the nanoshell. Encapsulation of the enzyme tyrosinase lead to the confinement of toxic melanin production for robust detection via multispectral optoacoustic tomography (MSOT). Co-expression of ferritin-like native cargo (EncB or EncC) resulted in efficient iron sequestration that produced substantial contrast by magnetic resonance imaging (MRI) and enabled magnetic cell sorting. The monodisperse, spherical, and iron-loading nanoshells also proved to be excellent genetically encoded markers for cryo-electron tomography (cryo-ET). In general, eukaryotically expressed encapsulins enable cellular engineering of spatially confined multicomponent processes with versatile applications in multiscale molecular imaging, as well as intriguing implications for metabolic engineering and cellular therapy.

synthetic biology↗