Biology subjects

Bak, A.

Publications and source records attributed to Bak, A..

10 recordsLinked to original sources

bioRxiv2026

Graph theory for the analysis of micro-electrode array recordings of human brain slices - framework and benchmarking

Micro-electrode array (MEA) recordings are widely used to characterize functional connectivity in neural cultures and have gained traction for the analysis of human brain slices. However, the impact of graph construction methodology on the resulting network topology has not been systematically quantified. Here, we benchmark three methods - shared spiking activity, Pearson cross-correlation, and the spike time tiling coefficient (STTC) - across 37 recordings from human cortical slice cultures classified into low, moderate, and high activity groups. We show that method choice alone produces large topological differences (Cohens d = 0.86-1.14 for clustering coefficient, d > 1.0 for node count), while higher-order features such as modularity remain stable. Each method exhibits a distinct sensitivity profile: shared spiking detects activity-dependent changes primarily through network size, correlation uniquely captures clustering differences, and STTC combines strong biological sensitivity with negligible parameter dependence across lag windows (all d < 0.1). Within shared spiking, z-score normalization dominates all other parameter choices (d > 1.0 versus bin size effects of d < 0.23), functioning as an implicit analytical null model that fundamentally reshapes the edge set rather than merely rescaling weights. Inter-method edge overlap is low (Jaccard index 0.08-0.45) and activity dependent, demonstrating that these methods identify substantially different connections from identical data. Our results reveal that methodological choices including construction method, threshold, and normalization introduce hidden degrees of freedom with effect sizes comparable to the biological signals being measured. We provide practical recommendations for parameter selection, reporting, and cross-method validation in MEA-based network neuroscience. Author SummaryWhen we record electrical activity from brain tissue using grids of electrodes, we can ask how different sites influence one another and map the tissue as a network of connections. Thanks to novel culturing methods, this approach is increasingly used to study human brain slices. However, deciding what is "connected" is not well defined. Researchers use several different methods, and it has never been clear how much this choice shapes the network they end up describing. Here we compared three widely used methods on 37 recordings from human cortical slices spanning a range of activity levels. We found that the method alone can change the apparent structure of the network as much as real biological differences do. The methods frequently disagreed about which connections exist and some technical choices, including normalization techniques, had surprisingly large effects. Because these hidden choices can rival the biological signal, we provide this benchmarking work with practical recommendations for selecting, reporting, and cross-checking methods, so that network studies of brain tissue become more transparent, comparable, and reproducible.

neuroscience↗

bioRxiv2026

Reversible peptide self-assembly enables sustained drug delivery with tuneable pharmacokinetics

Therapeutic peptides combine high target specificity with potent biological activity.1 However, treatment success is often limited by rapid clearance and the need for frequent injections.2, 3 This challenge is particularly acute for therapeutic peptides used in obesity, where clinical benefit must be balanced against dose-dependent adverse effects. In nature, these constraints are overcome by storing hormones as reversible fibrils,4 but pharmacokinetic control is essential for widespread adoption of bio-inspired self-assembled depots for therapeutic peptides. Here, we show that tuneable pharmacokinetics can be achieved and modelled by mapping the fundamental chemical parameters of reversibly self-assembly in vitro. We demonstrate this approach for the amylin analogue pramlintide. Amylin analogues are under development for the next generation of diabetes and obesity treatments, with improved mechanism of action e.g. preserving lean body mass.5-8 Pramlintide is an approved drug with a well-established safety profile, however, it has a comparable half-life to native amylin.8-12 In a pilot study, we achieve in vitro-in vivo correlation, increasing the half-life of pramlintide 20-82-fold in rats, while controlling burst release. These findings demonstrate that the optimisation of pharmacokinetics can be decoupled from peptide engineering, establishing a generalisable framework for generating long-acting peptide formulations by emulating native storage mechanisms.

biophysics↗

bioRxiv2026

Pathological stiffening by crosslinking glycation of titin

Heterogeneous, non-enzymatic glycation chemistry triggered by sugar-derived metabolites is typical of diseases that also entail pathological stiffening of cells, such as diabetes and age-related disorders. However, the mechanisms responsible for cell stiffening and the role of glycated biomolecules remain largely unexplored. Here, we show that glycation of cardiac titin, a giant intracellular protein scaffolding contractile sarcomeres, is increased in diabetes and leads to rigidification of both the protein and cardiomyocytes. Mechanistically, glycation-induced titin stiffening results from decreased contour length and enhanced folding of otherwise structurally intact protein domains following extensive formation of intramolecular crosslinking advanced glycation end products (AGEs). These stiffening effects outweigh softening contributions by competing, non-crosslinking AGEs. In combination, our work overcomes the intrinsic chemical complexity typical of glycation to uncover crosslinking AGEs as a source of pathological stiffening of cells, which we propose contributes to tissue dysfunction in situations of glycative stress.

biophysics↗

bioRxiv2024

Comprehensive Analysis of Human Dendritic Spine Morphology and Density: Exploring Diversity of Human Dendritic Spines

Dendritic spines, small protrusions on neuronal dendrites, play a crucial role in brain function by changing shape and size in response to neural activity. So far, in depth analysis of dendritic spines in human brain tissue is lacking. This study presents a comprehensive analysis of human dendritic spine morphology and density using a unique dataset from human brain tissue from 27 patients (8 females, 19 males, aged 18-71) undergoing tumor or epilepsy surgery at three neurosurgery sites. We used acute slices and organotypic brain slice cultures to examine dendritic spines, classifying them into the three main morphological subtypes: Mushroom, Thin, and Stubby, via 3D reconstruction using ZEISS arivis Pro software. A deep learning model, trained on 39 diverse datasets, automated spine segmentation and 3D reconstruction, achieving a 74% F1-score and reducing processing time by over 50%. We show significant differences in spine density by sex, dendrite type, and tissue condition. Females had higher spine densities than males, and apical dendrites were denser in spines than basal ones. Acute tissue showed higher spine densities compared to cultured human brain tissue. With time in culture, Mushroom spines decreased, while Stubby and Thin spine percentages increased, particularly from 7-9 to 14 days in vitro, reflecting potential synaptic plasticity changes. Our study underscores the importance of using human brain tissue to understand unique synaptic properties and shows that integrating deep learning with traditional methods enables efficient large-scale analysis, revealing key insights into sex- and tissue-specific dendritic spine dynamics relevant to neurological diseases. New and NoteworthyThis study presents a dataset of nearly 4,000 morphologically reconstructed human dendritic spines across different ages, gender, and tissue conditions. The dataset was further used to evaluate a deep learning algorithm for three-dimensional spine reconstruction, offering a scalable method for semi-automated spine analysis across various tissues and microscopy setups. The findings enhance understanding of human neurology, indicating potential connections between spine morphology, brain function, and the mechanisms of neurological and psychiatric diseases.

neuroscience↗

bioRxiv2024

Dysregulated Skeletal Muscle Myosin Super-relaxation in Type II, but Not Type I, Diabetes Mellitus

Disrupted energy balance is critical for the onset and development of Type II diabetes. The exact underlying metabolic mechanisms remain incomplete but skeletal muscle is thought to play an important pathogenic role. As the super-relaxed state of its most abundant protein, myosin, regulates cellular energetics, here, we aimed to investigate whether it is altered in patients with type II diabetes. For that, we used vastus lateralis biopsy specimens (obtained from patients with type II diabetes and matched controls) and run a combination of structural and functional assays consisting of loaded Mant-ATP chase experiments, X-ray diffraction and LC-MS/MS proteomics in isolated muscle fibres. Our studies revealed a greater muscle myosin super-relaxation and decreased cellular ATP demand in patients than controls. Subsequent proteomic analyses indicated that these (mal)adaptations likely originated from remodeled sarcomeric proteins and greater myosin glycation levels in patients than controls. Overall, our findings emphasize a complex molecular dysregulation of myosin super-relaxed state and energy consumption in type II diabetes. Ultimately, pharmacological targeting of myosin could benefit skeletal muscle and whole-body metabolic health through the enhancement of ATP consumption. Significance StatementMyosin super-relaxation, essential for the regulation of skeletal muscle metabolic rate, is disrupted in type II diabetes due to protein hyper-glycation. As a consequence, myosin ATP demand is significantly lowered. Overall, our findings provide a strong rationale for the use of activators of myosin ATPase to enhance basal energy expenditure in type II diabetes.

cell biology↗

bioRxiv2023

Long-term human organotypic brain slice cultures: a detailed protocol to provide a comprehensive framework for single-neuron and neuronal network investigations

BackgroundThe investigation of the human brain at cellular and microcircuit level remains challenging due to the fragile viability of neuronal tissue, inter- and intra-variability of the samples and limited availability of human brain material. New methodHere, we present an optimized work-up to use resected tissue from brain surgeries for live cell experiments in vitro. Comparison with existing methodsWe provide a reworked, detailed protocol of the production, culturing and viral transduction of human organotypic brain slice cultures for research purposes. ResultsWe highlight the critical pitfalls of the culturing process of the human brain tissue and present results on viral expression, single-cell Patch-Clamp recordings, as well as multi-electrode array recordings over a prolonged period of time. Additionally, our statistics show that brain tissue from patients of any age and morbidity can be used for organotypic brain slice cultures if carefully selected. ConclusionsOrganotypic brain slice cultures are of great value for basic neuroscience and disease modeling over a time course of three weeks. HighlightsO_LILong-term human organotypic brain slice cultures are viable for 2-3 weeks and provide a framework for basic neuroscience and disease modeling C_LIO_LIWe provide a reworked, detailed protocol for organotypic human brain slice culture production and maintenance C_LIO_LIWe show results of long-term culturing of human organotypic brain slice cultures in terms of viral transduction, whole-cell Patch-Clamp recordings and multi-electrode array recordings C_LIO_LIStatistics of 16 surgeries show the correlation between the overall success rates of efficient culturing and viral transduction with the patient age and morbidity C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/561508v1_fig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@17c985aorg.highwire.dtl.DTLVardef@f651fdorg.highwire.dtl.DTLVardef@180d32eorg.highwire.dtl.DTLVardef@a896b5_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1, Graphical abstract.C_FLOATNO Schematic overview of preparation, maintenance and experimental workup of human organotypic brain slice cultures. After surgical resection, human brain tissue is prepared, sliced and cultured at air-liquid-interface between human cerebrospinal fluid and defined incubator atmosphere, allowing for week-long viability. This enables extensive experimental workup such as viral transduction, single cell and multi-electrode array electrophysiological recordings. C_FIG

neuroscience↗

bioRxiv2023

Modulation of Giant Depolarizing Potentials (GDPs) in Human Large Basket Cells by Norepinephrine and Acetylcholine

Rhythmic brain activity has been implicated in many brain functions and it is sensible to neuromodulation, but so far very few studies have investigated this activity on the cellular level in vitro in human tissue samples. In this study we revealed and characterized a novel rhythmic network activity in human neocortex. Intracellular patch-clamp recordings showed that giant depolarizing potentials (GDPs) were frequently found in human cortical neurons. GDPs appeared in a low frequency band ([~] 0.3 Hz) similar to that described for slow oscillations in vivo and displayed large amplitudes and long decay times. Under the same experimental conditions, no rhythmic activity was found in L2/3 of the rat neocortex. GDPs were predominantly observed in a subset of L2/3 interneurons considered to be large basket cells based on previously described morphological features. In addition, GDPs are highly sensitive to norepinephrine (NE) and acetylcholine (ACh), two neuromodulators known to modulate low frequency oscillations. NE increased the frequency of the GDPs by enhancing {beta}-adrenergic receptor activity while ACh decreased GDP frequency through M4 muscarinic receptor-activation. Multi-electrode array (MEA) recordings demonstrated that NE promoted synchronous oscillatory network activity while the application of ACh led to a desynchronization of neuronal activity. Our data indicate that the human neocortex is more prone to generate slow wave activity, which was reflected by more pronounced GDPs in L2/3 large basket cells. The distinct modulation of GDPs and slow wave activity by NE and ACh exerts a specific modulatory control over the human neocortex.

neuroscience↗

bioRxiv2021

RNA viral communities are structured by host plant phylogeny in oak and conifer leaves

Wild plants can suffer devastating diseases, experience asymptomatic, persistent infections, and serve as reservoirs for viruses of agricultural crops, yet we have a limited understanding of the natural plant virosphere. To access representatives of locally and globally distinct wild plants and investigate their viral diversity, we extracted and sequenced dsRNA from leaves from 16 healthy oak and conifer trees in the UC Davis Arboretum (Davis, California). From de novo assemblies, we recovered 389 RNA-dependent RNA polymerase (RdRp) gene sequences from 384 putative viral species, and a further 580 putative viral contigs were identified with virus prediction software followed by manual confirmation of virus annotation. Based on similarity to known viruses, most recovered viruses were predicted to infect plants or fungi, with the highest diversity and abundance observed in the Totiviridae and Mitoviridae families. Phyllosphere viral community composition differed significantly by host plant phylogeny, suggesting the potential for host-specific viromes. The phyllosphere viral community of one oak tree differed substantially from other oak viral communities and contained a greater proportion of putative mycoviral sequences, potentially due to the trees more advanced senescence at the time of sampling. These results suggest that oaks and conifers harbor a vast diversity of viruses with as-yet unknown roles in plant health and phyllosphere microbial ecology.

ecology↗

bioRxiv2020

Endosomal escape of delivered mRNA from endosomal recycling tubules visualized at the nanoscale

Delivery of exogenous mRNA using lipid nanoparticles (LNP) is a promising strategy for therapeutics. However, a bottleneck remains the poor understanding of the parameters that correlate with endosomal escape vs. cytotoxicity. To address this problem, we compared the endosomal distribution of six LNP-mRNA formulations of diverse chemical composition and efficacy, similar to those employed in mRNA-based vaccines, in primary human adipocytes, fibroblasts and HeLa cells. Surprisingly, we found that total uptake is not a sufficient predictor of delivery and different LNP vary considerably in endosomal distributions. Prolonged uptake impaired endosomal acidification, a sign of cytotoxicity, and caused mRNA to accumulate in compartments defective in cargo transport and unproductive for delivery. In contrast, early endocytic/recycling compartments have the highest probability for mRNA escape. By super-resolution microscopy we could resolve single LNP-mRNA within sub-endosomal compartments and capture events of mRNA escape from endosomal recycling tubules. Our results change the view of the mechanisms of endosomal escape and define quantitative parameters to guide the development of mRNA formulations towards higher efficacy and lower cytotoxicity.

bioengineering↗

bioRxiv2020

Optimizing the PBS1 Decoy System to Confer Resistance to Potyvirus Infection in Arabidopsis and Soybean

The Arabidopsis resistance protein RPS5 is activated by proteolytic cleavage of the protein kinase PBS1 by the Pseudomonas syringae effector protease AvrPphB. We have previously shown that replacing seven amino acids at the cleavage site of PBS1 with a motif cleaved by the NIa protease of turnip mosaic virus (TuMV) enables RPS5 activation upon TuMV infection. However, this engineered resistance conferred a trailing necrosis phenotype indicative of a cell death response too slow to contain the virus. We theorized this could result from a positional mismatch within the cell between PBS1TuMV, RPS5 and the NIa protease. To test this, we re-localized PBS1TuMV and RPS5 to cellular sites of NIa accumulation. These experiments revealed that relocation of RPS5 away from the plasma membrane compromised RPS5-dependent cell death in N. benthamiana, even though PBS1 was efficiently cleaved. As an alternative approach, we tested whether overexpression of plasma membrane-localized PBS1TuMV would enhance RPS5 activation by TuMV. Significantly, over-expressing the PBS1TuMV decoy protein conferred complete resistance to TuMV when delivered by either Agrobacterium or by aphid transmission, showing that RPS5-mediated defense responses are effective against bacterial and viral pathogens. Lastly, we have now extended this PBS1 decoy approach to soybean by modifying a soybean PBS1 ortholog to be cleaved by the NIa protease of soybean mosaic virus (SMV). Transgenic overexpression of this soybean PBS1 decoy conferred immunity to SMV, demonstrating that we can use endogenous PBS1 proteins in crop plants to engineer economically relevant disease resistant traits.

plant biology↗