Biology subjects

Lenz, M.

Publications and source records attributed to Lenz, M..

29 records · Page 2Linked to original sources

bioRxiv2020

Selecting stimulation intensity in repetitive transcranial magnetic stimulation studies: A systematic review between 1991 and 2020

BackgroundRepetitive transcranial magnetic stimulation (rTMS) is an increasingly used, non-invasive brain stimulation technique in neuroscience research and clinical practice with a broad spectrum of suggested applications. Among other parameters, the choice of stimulus intensity and intracranial electric field strength substantially impact rTMS outcome. This review provides a systematic overview of the intensity selection approaches and stimulation intensities used in human rTMS studies. We also examined whether studies report sufficient information to reproduce stimulus intensities in basic science research models. Methods. We performed a systematic review by focusing on original studies published between 1991 and 2020. We included conventional (e.g., 1 Hz or 10 Hz) and patterned protocols (e.g., continuous or intermittent theta burst stimulation). We identified 3,784 articles in total, and we manually processed a representative portion (20%) of randomly selected articles. Results. The majority of the analyzed studies (90% of entries) used the motor threshold (MT) approach and stimulation intensities from 80 to 120% of the MT. For continuous and intermittent theta burst stimulation, the most frequent stimulation intensity was 80% of the active MT. Most studies (92% of entries) did not report sufficient information to reproduce the stimulation intensity. Only a minority of studies (1.03% of entries) estimated the rTMS-induced electric field strengths. Conclusion. We formulate easy-to-follow recommendations to help scientists and clinicians report relevant information on stimulation intensity. Future standardized reporting guidelines may facilitate the use of basic science approaches aiming at better understanding the molecular, cellular, and neuronal mechanisms of rTMS.

neuroscience↗

bioRxiv2020

All-Trans Retinoic Acid induces synaptic plasticity in human cortical neurons

A defining feature of the brain is its ability to adapt structural and functional properties of synaptic contacts in an experience-dependent manner. In the human cortex direct experimental evidence for synaptic plasticity is currently missing. Here, we probed plasticity in human cortical slices using the vitamin A derivative all-trans retinoic acid, which has been suggested as medication for the treatment of neuropsychiatric disorders, e.g., Alzheimers disease. Our experiments demonstrate coordinated structural and functional changes of excitatory synapses of superficial (layer 2/3) pyramidal neurons in the presence of all-trans retinoic acid. This synaptic adaptation is accompanied by ultrastructural remodeling of the calcium-storing spine apparatus organelle and requires mRNA-translation. We conclude that all-trans retinoic acid is a potent mediator of synaptic plasticity in the adult human cortex.

neuroscience↗

bioRxiv2020

Local structure of DNA toroids reveals curvature-dependent intermolecular forces

In viruses and cells, DNA is closely packed and tightly curved thanks to polyvalent cations inducing an effective attraction between its negatively charged filaments. Our understanding of this effective attraction remains very incomplete, partly because experimental data is limited to bulk measurements on large samples of mostly uncurved DNA helices. Here we use cryo electron microscopy to shed light on the interaction between highly curved helices. We find that the spacing between DNA helices in spermine-induced DNA toroidal condensates depends on their location within the torus, consistent with a mathematical model based on the competition between electrostatic interactions and the bending rigidity of DNA. We use our model to infer the characteristics of the interaction potential, and find that its equilibrium spacing strongly depends on the curvature of the filaments. In addition, the interaction is much softer than previously reported in bulk samples using different salt conditions. Beyond viruses and cells, our characterization of the interactions governing DNA-based dense structures could help develop robust designs in DNA nanotechnologies.

biophysics↗

bioRxiv2019

Anisotropic ESCRT-III architecture governs helical membrane tube formation

ESCRT-III proteins assemble into ubiquitous membrane-remodeling polymers during many cellular processes. Here we describe the structure of helical membrane tubes that are scaffolded by bundled ESCRT-III filaments. Cryo-ET reveals how the shape of the helical membrane tube arises from the assembly of distinct bundles of protein filaments that bind the membrane with different mean curvatures. Cryo-EM reveals how one of these ESCRT-III filaments engages the membrane tube through a novel interface. Mathematical modeling of the helical membrane tube suggests how its shape emerges from differences in membrane binding energy, positional rigidity, and membrane tension. Altogether, our findings support a model in which increasing the rigidity of ESCRT-III filaments through the assembly of multi-strands triggers buckling of the membrane.\n\nOne Sentence SummaryESCRT-III heteropolymers deform membranes into helical tubes.

biochemistry↗

bioRxiv2019

Actin modulates shape and mechanics of tubular membranes

The actin cytoskeleton shapes cells and also organizes internal membranous compartments. In particular, it interacts with membranes in intracellular transport of material in mammalian cells, yeast or plant cells. Tubular membrane intermediates, pulled along microtubule tracks, are involved during these processes, and destabilize into vesicles. While the role of actin in this destabilization process is still debated, literature also provide examples of membranous structures stabilization by actin. To directly address this apparent contradiction, we mimic the geometry of tubular intermediates with preformed membrane tubes. The growth of an actin sleeve at the tube surface is monitored spatio-temporally. Depending on network cohesiveness, actin is able to stabilize, or maintain membrane tubes under pulling. Indeed, on a single tube, thicker portions correlate with the presence of actin. Such structures relax over several minutes, and may provide enough time and curvature geometries for other proteins to act on tube stability.

biophysics↗

bioRxiv2019

A low-cost fluorescence reader for in vitro transcription and nucleic acid detection with Cas13a

Point-of-care testing (POCT) in low-resource settings requires tools that can operate independent of typical laboratory infrastructure. Due to its favorable signal-to-background ratio, a wide variety of biomedical tests utilize fluorescence as a readout. However, fluorescence techniques often require expensive or complex instrumentation and can be difficult to adapt for POCT. To address this issue, we developed a pocket-sized fluorescence detector costing less than $15 that is easy to manufacture and can operate in low-resource settings. It is built from standard electronic components, including an LED and a light dependent resistor, filter foils and 3D printed parts, and reliably detected less than 10 nM fluorescein concentrations (with a lower limit of detection of {approx}6.8 nM), which is sufficient to follow typical biochemical reactions used in POCT applications. All assays are conducted on filter paper, which allows for a flat detector architecture to improve signal collection. We validate the device by quantifying in vitro RNA transcription and also demonstrate sequence-specific detection of target RNAs in the nanomolar range using a Cas13a-based fluorescence assay. Cas13a is a RNA-guided, RNA-targeting CRISPR effector with promiscuous RNase activity upon recognition of its RNA target. Cas13a sensing is highly specific and adaptable and in combination with our detector represents a promising approach for nucleic acid POCT. Furthermore, our open-source device architecture could be a valuable educational tool that integrates hardware, software and biochemistry concepts.

bioengineering↗

bioRxiv2018

Adipose tissue in health and disease through the lens of its building blocks

BackgroundHighly specialized cells work in synergy forming tissues to perform functions required for the survival of organisms. Understanding this tissue-specific cellular heterogeneity and homeostasis is essential to comprehend the development of diseases within the tissue and also for developing regenerative therapies. Cellular subpopulations in the adipose tissue have been related to disease development, but efforts towards characterizing the adipose tissue cell type composition are limited due to lack of robust cell surface markers, limited access to tissue samples, and the labor-intensive process required to identify them.\n\nResultsWe propose a framework, identifying cellular heterogeneity while providing state-of-the-art cellular markers for each cell type present in tissues using transcriptomics level analysis. We validate our approach with an independent dataset and present the most comprehensive study of adipose tissue cell type composition to date, determining the relative amounts of 21 different cell types in 779 adipose tissue samples detailing differences across four adipose tissue depots, between genders, across ranges of BMI and in different stages of type-2 diabetes. We also highlight the heterogeneity in reported marker-based studies of adipose tissue cell type composition and provide novel cellular markers to distinguish different cell types within the adipose tissue.\n\nConclusionsOur study provides a systematic framework for studying cell type composition in a given tissue and valuable insights into adipose tissue cell type heterogeneity in health and disease.

systems biology↗

bioRxiv2018

A direct proof that sole actin dynamics drive membrane deformations

Cell membrane deformations are crucial for proper cell function. Specialized protein assemblies initiate inward or outward membrane deformations that turn into, for example, filopodia or endocytic intermediates. Actin dynamics and actin-binding proteins are involved in this process, although their detailed role remains controversial. We show here that a dynamic, branched actin network is sufficient, in absence of any membrane-associated proteins, to initiate both inward and outward membrane deformation. With actin polymerization triggered at the membrane of liposomes, we produce inward filopodia-like structures at low tension, while outward endocytosis-like structures are robustly generated regardless of tension. Our results are reminiscent of endocytosis in mammalian cells, where actin polymerization forces are required when membrane tension is increased, and in yeast, where they are always required to overcome the opposing turgor pressure. By combining experimental observations with physical modeling, we propose a mechanism for actin-driven endocytosis under high tension or high pressure conditions.

biophysics↗

bioRxiv2017

Modulation of formin processivity by profilin and mechanical tension

Formins are major regulators of actin networks. They enhance actin filament dynamics by remaining processively bound to filament barbed ends. How biochemical and mechanical factors affect formin processivity are open questions. Monitoring individual actin filaments in a microfluidic flow, we report that formin mDia1 dissociates faster under higher ionic strength and when actin concentration is increased. Profilin, known to increase the elongation rate of formin-associated filaments, surprisingly decreases the formin dissociation rate, by bringing formin FH1 domains in transient contact with the barbed end. In contrast, piconewton tensile forces applied to actin filaments accelerate formin dissociation by orders of magnitude, largely overcoming profilin-mediated stabilization. We developed a model of formin conformations and its confrontation to our data indicates the existence of two different dissociation pathways, with force favoring one over the other. How cells limit formin dissociation under tension is now a key question for future studies.

biophysics↗

bioRxiv2017

Leukocyte counts based on site-specific DNA methylation analysis

The composition of white blood cells is usually assessed by histomorphological parameters or flow cytometric measurements. Alternatively, leukocyte differential counts (LDCs) can be estimated by deconvolution algorithms for genome-wide DNA methylation (DNAm) profiles. We identified cell-type specific CG dinucleotides (CpGs) that facilitate relative quantification of leukocyte subsets. Site-specific analysis of DNAm levels by pyrosequencing provides similar precision of LDCs as conventional methods, whereas it is also applicable to frozen samples and requires only very small volumes of blood. Furthermore, we describe a new approach for absolute quantification of cell numbers based on a non-methylated reference DNA. Our \"Epi-Blood-Count\" facilitates robust and cost effective analysis of blood counts for clinical application.

molecular biology↗

bioRxiv2017

Stem cell differentiation is a stochastic process with memory

Pluripotent stem cells are able to self-renew indefinitely in culture and differentiate into all somatic cell types in vivo. While much is known about the molecular basis of pluripotency, the molecular mechanisms of lineage commitment are complex and only partially understood. Here, using a combination of single cell profiling and mathematical modeling, we examine the differentiation dynamics of individual mouse embryonic stem cells (ESCs) as they progress from the ground state of pluripotency along the neuronal lineage. In accordance with previous reports we find that cells do not transit directly from the pluripotent state to the neuronal state, but rather first stochastically permeate an intermediate primed pluripotent state, similar to that found in the maturing epiblast in development. However, analysis of rate at which individual cells enter and exit this intermediate metastable state using a hidden Markov model reveals that the observed ESC and epiblast-like macrostates conceal a chain of unobserved cellular microstates, which individual cells transit through stochastically in sequence. These hidden microstates ensure that individual cells spend well-defined periods of time in each functional macrostate and encode a simple form of epigenetic memory that allows individual cells to record their position on the differentiation trajectory. To examine the generality of this model we also consider the differentiation of mouse hematopoietic stem cells along the myeloid lineage and observe remarkably similar dynamics, suggesting a general underlying process. Based upon these results we suggest a statistical mechanics view of cellular identities that distinguishes between functionally-distinct macrostates and the many functionally-similar molecular microstates associated with each macrostate. Taken together these results indicate that differentiation is a discrete stochastic process amenable to analysis using the tools of statistical mechanics.

systems biology↗