Biology subjects

Pfeiffer, M.

Publications and source records attributed to Pfeiffer, M..

8 recordsLinked to original sources

bioRxiv2024

Spring-loaded DNA origami arrays as energy-supplied hardware for modular nanorobots

DNA origami nanodevices allow us to mimic cellular functions in a rationally controlled manner. They describe machineries which respond to environmental stimuli by conducting different tasks. To date, this mostly is achieved by constructing conformational two-state switches which upon activation by stimuli change their conformation resulting in the performance of a priorly programmed task. Their applicability however is often limited to a single, specific stimuli - output combination due to their intrinsic properties as two-state systems only. This makes expanding them further to include multiple stimuli/ outputs challenging. Here, we address this problem by introducing reconfigurable DNA origami arrays as a coupled network of two-state systems. We use this network to create a universal design strategy in which different operational units can be incorporated into any two-state system of our nanorobot. The resulting nanorobot is capable of receiving different stimuli, computing the response to the received stimuli using multi-level Boolean logic gating and yielding multiple programmed output operations with controlled order, timing and spatial position. We expect that this strategy will be a crucial step towards further developing DNA origami nanorobots for applications in various technological fields.

biophysics↗

bioRxiv2023

Modulation of Human Frontal Midline Theta by Neurofeedback: A Systematic Review and Quantitative Meta-Analysis

Human brain activity consists of different frequency bands associated with varying functions. Oscillatory activity of frontal brain regions in the theta range (4-8Hz) is linked to cognitive processing and can be modulated by neurofeedback - a technique where participants receive real-time feedback about their brain activity and learn to modulate it. However, criticism of this technique evolved, and high heterogeneity of study designs complicates a valid evaluation of its effectiveness. This meta-analysis provides the first systematic overview over studies attempting to modulate frontal midline theta with neurofeedback in healthy human participants. Out of 1431 articles screened, 14 studies were eligible for systematic review and 11 for quantitative meta-analyses. Studies were evaluated following the DIAD model and the PRISMA guidelines. A significant across-study effect of medium size (Hedges g = .66; 95%-CI [-0.62, 1.73]) with substantial between-study heterogeneity (Q(16) = 167.43, p < .0001) was observed and subanalysis revealed effective frontal midline theta upregulation. We discuss moderators of effect sizes and provide guidelines for future research in this dynamic field.

neuroscience↗

bioRxiv2023

Engineering Modular and Tunable Single Molecule Sensors by Decoupling Sensing from Signal Output

Biosensors play key roles in medical research and diagnostics, but there currently is a lack of sensing platforms that combine easy adaptation to new targets, strategies to tune the response window to relevant analyte concentration ranges and allow for the incorporation of multiple sensing elements to benefit from multivalency. Utilizing a DNA origami nanostructure as a scaffold for arranging the different sensor components, we here propose an approach for the development of modular and tunable single-molecule sensors capable of detecting a variety of biomolecular targets such as nucleic acids, antibodies and restriction enzymes while offering mechanisms to tune the dynamic window, the specificity, and the cooperativity of the sensor.

biophysics↗

bioRxiv2020

Addressable Nanoantennas with Cleared Hotspots for Single-Molecule Detection on a Portable Smartphone Microscope

The advent of highly sensitive photodetectors1,2 and the development of photostabilization strategies3 made detecting the fluorescence of a single molecule a routine task in many labs around the world. However, to this day, this process requires cost-intensive optical instruments due to the truly nanoscopic signal of a single emitter. Simplifying single-molecule detection would enable many exciting applications, e.g. in point-of-care diagnostic settings, where costly equipment would be prohibitive.4 Here, we introduce addressable NanoAntennas with Cleared HOtSpots (NACHOS) that are scaffolded by DNA origami nanostructures and can be specifically tailored for the incorporation of bioassays. Single emitters placed in the NACHOS emit up to 461-fold brighter enabling their detection with a customary smartphone camera and an 8-US-dollar objective lens. To prove the applicability of our system, we built a portable, battery-powered smartphone microscope and successfully carried out an exemplary single-molecule detection assay for DNA specific to antibiotic-resistant Klebsiella pneumonia "on the road ".

biophysics↗

bioRxiv2019

Identification of a fatty acid-sensitive interaction between mitochondrial uncoupling protein 3 and enoyl-CoA hydratase 1 in skeletal muscle

Skeletal muscle mitochondrial fatty acid (FA) overload in response to chronic overnutrition is a prominent pathophysiological mechanism in obesity-induced metabolic disease. Increased disposal of FAs is therefore an attractive strategy for intervening in obesity and related disorders. Skeletal muscle uncoupling protein 3 (UCP3) activity is associated with increased FA oxidation and antagonizes weight gain in mice on obesogenic diets, but the mechanisms involved are not clear. Here, we show that UCP3 forms a direct, FA-stimulated, mitochondrial matrix-localized complex with the auxiliary unsaturated FA-metabolizing enzyme, {Delta}3,5-{Delta}2,4dienoyl-CoA-isomerase (ECH1). Expression studies in C2C12 myoblasts that functionally augments state 4 (uncoupled) respiration and FA oxidation in skeletal myocytes.\n\nMechanistic studies indicate that ECH1:UCP3 complex formation is likely stimulated by FA import into the mitochondria to enhance uncoupled respiration and unsaturated FA oxidation in mouse skeletal myocytes. In order to characterize the contribution of ECH1-dependent FA metabolism in NST, we generated an ECH1 knockout mouse and found that these mice were severely cold intolerant, despite an up-regulation of UCP3 expression in SKM. These findings illuminate a novel mechanism that links unsaturated FA metabolism with mitochondrial uncoupling and non-shivering thermogenesis in SKM.

biochemistry↗

bioRxiv2018

In-depth investigation of the species problem and taxonomic status of marbled crayfish, the first asexual decapod crustacean

The marbled crayfish is the only obligately parthenogenetic decapod crustacean and a novel research model and invasive animal on three continents. It is regarded either as a parthenogenetic form of slough crayfish Procambarus fallax or as a separate species named Procambarus virginalis. In order to investigate the species question of this unusual crayfish in detail we have identified the similarities and differences in morphology, life history, genetics, behaviour, ecology and biogeography between marbled crayfish and its most likely parent species P. fallax. We have investigated specimens from natural habitats, laboratory colonies and museum collections and performed a meta-analysis of our data and published data. Our COI based molecular tree with 27 Cambaridae confirms closest relationship of marbled crayfish with P. fallax. Marbled crayfish and P. fallax are similar with respect to morphological characters, coloration and body proportions, but differ considerably with respect to body size, fertility and longevity. The mitochondrial genes of both crayfish are similar, but ploidy level and haploid genome size are markedly different. Both crayfish are eurytopic and have two major annual recruitment periods, but marbled crayfish show different population structure and higher invasiveness. Marbled crayfish occur in tropical to cold temperate habitats of the old world, but P. fallax is confined to subtropical and warm-temperate habitats of the southeastern USA. Cross-breeding experiments with both crayfish revealed reproductive isolation. The application of the Evolutionary Genetic Species Concept for asexuals to all available data supports raising marbled crayfish from \"forma\" to species rank. A determination key is provided to discriminate Procambarus virginalis, the first asexual decapod species, from its parent species P. fallax.

zoology↗

bioRxiv2018

A Generative Growth Model for Thalamocortical Axonal Branching in Primary Visual Cortex

Axonal morphology displays large variability and complexity, yet the canonical regularities of the cortex suggest that such wiring is based on the repeated initiation of a small set of genetically encoded rules. Extracting underlying developmental principles can hence shed light on what genetically encoded instructions must be available during cortical development. Within a generative model, we investigate growth rules for axonal branching patterns in cat area 17, originating from the lateral geniculate nucleus of the thalamus. This target area of synaptic connections is characterized by extensive ramifications and a high bouton density, characteristics thought to preserve the spatial resolution of receptive fields and to enable connections for the ocular dominance columns. We compare individual and global statistics, such as a newly introduced asymmetry index and the global segment-length distribution, of generated and real branching patterns as the benchmark for growth rules. We show that the proposed model surpasses the statistical accuracy of the Galton-Watson model, which is the most commonly employed model for biological growth processes. In contrast to the Galton-Watson model, our model can recreate the log-normal segment-length distribution of the experimental dataset and is considerably more accurate in recreating individual axonal morphologies. To provide a biophysical interpretation for statistical quantifications of the axonal branching patterns, the generative model is ported into the physically accurate simulation framework of Cx3D. In this simulation environment we demonstrate how the proposed growth process can be formulated as an interactive process between genetic growth rules and chemical cues in the local environment.

neuroscience↗

bioRxiv2017

Conditioning by Subthreshold Synaptic Input Changes the Characteristic Firing Pattern of CA3 Hippocampal Neurons

Unlike synaptic strength, intrinsic excitability is assumed to be a stable property of neurons. For example, learning of somatic conductances is generally not incorporated into computational models, and the discharge pattern of neurons in response to test stimuli is frequently used as a basis for phenotypic classification. However, it is increasingly evident that signal processing properties of neurons are more generally plastic on the timescale of minutes. Here we demonstrate that the intrinsic firing patterns of CA3 neurons of the rat hippocampus in vitro undergo rapid long-term plasticity in response to a few minutes of only subthreshold synaptic conditioning. This plasticity on the spike-timing could also be induced by intrasomatic injection of subthreshold depolarizing pulses and was blocked by kinase inhibitors, indicating that discharge dynamics are modulated locally. Cluster analysis of firing patterns before and after conditioning revealed systematic transitions towards adapting and intrinsic burst behaviours, irrespective of the patterns initially exhibited by the cells. We used a conductance-based model to decide appropriate pharmacological blockade, and found that the observed transitions are likely due to recruitment of calcium and M-type potassium conductances. We conclude that CA3 neurons adapt their conductance profile to the subthreshold activity of their input, so that their intrinsic firing pattern is not a static signature, but rather a reflection of their history of subthreshold activity. In this way, recurrent output from CA3 neurons may collectively shape the temporal dynamics of their embedding circuits.\n\nNew & NoteworthyDespite being widely conserved across the animal phyla, it is still a mystery why nerve cells present diverse discharge dynamics upon somatic step currents. Adding a new timing dimension to the intrinsic plasticity literature, here we show that CA3 neurons rapidly adapt through the space of known firing patterns in response to the subthreshold signals that they receive from their embedding circuit. This result implies that CA3 neurons collectively adjust their network processing to the temporal statistics of their circuit.

neuroscience↗