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Background: The LDLR (low-density lipoprotein receptor) in the liver is the major determinant of LDL-cholesterol levels in human plasma. The discovery of genes that regulate the activity of LDLR helps to identify pathomechanisms of hypercholesterolemia and novel therapeutic targets against atherosclerotic cardiovascular disease. Methods: We performed a genome-wide RNA interference screen for genes limiting the uptake of fluorescent LDL into Huh-7 hepatocarcinoma cells. Top hit genes were validated by in vitro experiments as well as analyses of data sets on gene expression and variants in human populations. Results: The knockdown of 54 genes significantly inhibited LDL uptake. Fifteen of them encode for components or interactors of the U2-spliceosome. Knocking down any one of 11 out of 15 genes resulted in the selective retention of intron 3 of LDLR . The translated LDLR fragment lacks 88% of the full length LDLR and is detectable neither in nontransfected cells nor in human plasma. The hepatic expression of the intron 3 retention transcript is increased in nonalcoholic fatty liver disease as well as after bariatric surgery. Its expression in blood cells correlates with LDL-cholesterol and age. Single nucleotide polymorphisms and 3 rare variants of one spliceosome gene, RBM25 , are associated with LDL-cholesterol in the population and familial hypercholesterolemia, respectively. Compared with overexpression of wild-type RBM25 , overexpression of the 3 rare RBM25 mutants in Huh-7 cells led to lower LDL uptake. Conclusions: We identified a novel mechanism of posttranscriptional regulation of LDLR activity in humans and associations of genetic variants of RBM25 with LDL-cholesterol levels.

Image data are universal in life sciences research. Their proper handling is not. A significant proportion of image data in research papers show signs of mishandling that undermine their interpretation. We propose that a precise description of the image processing and analysis applied is required to address this problem. A new norm for reporting reproducible image analyses will diminish mishandling, as it will alert co-authors, referees, and journals to aberrant image data processing or, if published nonetheless, it will document it to the reader. To promote this norm, we discuss the effectiveness of this approach and give some step-by-step instructions for publishing reproducible image data processing and analysis workflows., The EMBO Journal, 40 (3), ISSN:0261-4189, ISSN:1460-2075

We introduce the NEUBIAS Gateway, a new platform for publishing materials related to bioimage analysis, an interdisciplinary field bridging computer science and life sciences. This emerging field has been lacking a central place to share the efforts of the growing group of scientists addressing biological questions using image data. The Gateway welcomes a wide range of publication formats including articles, reviews, reports and training materials. We hope the Gateway further supports this important field to grow and helps more biologists and computational scientists learn about and contribute to these efforts.

Due to their involvement in many physiologic and pathologic processes, there is a great interest in identifying new molecular pathways that mediate the formation and function of blood and lymphatic vessels. Vascular research increasingly involves the image-based analysis and quantification of vessel networks in tissue whole-mounts or of tube-like structures formed by cultured endothelial cells in vitro. While both types of experiments deliver important mechanistic insights into (lymph)angiogenic processes, the manual analysis and quantification of such experiments are typically labour-intensive and affected by inter-experimenter variability. To bypass these problems, we developed AutoTube, a new software that quantifies parameters like the area covered by vessels, vessel width, skeleton length and branching or crossing points of vascular networks in tissues and in in vitro assays. AutoTube is freely downloadable, comprises an intuitive graphical user interface and helps to perform otherwise highly time-consuming image analyses in a rapid, automated and reproducible manner. By analysing lymphatic and blood vascular networks in whole-mounts prepared from different tissues or from gene-targeted mice with known vascular abnormalities, we demonstrate the ability of AutoTube to determine vascular parameters in close agreement to the manual analyses and to identify statistically significant differences in vascular morphology in tissues and in vascular networks formed in in vitro assays., Angiogenesis, 22 (2)

Sinusoidal endothelial cells and mesenchymal CXCL12-abundant reticular cells are principal bone marrow stromal components, which critically modulate haematopoiesis at various levels, including haematopoietic stem cell maintenance. These stromal subsets are thought to be scarce and function via highly specific interactions in anatomically confined niches. Yet, knowledge on their abundance, global distribution and spatial associations remains limited. Using three-dimensional quantitative microscopy we show that sinusoidal endothelial and mesenchymal reticular subsets are remarkably more abundant than estimated by conventional flow cytometry. Moreover, both cell types assemble in topologically complex networks, associate to extracellular matrix and pervade marrow tissues. Through spatial statistical methods we challenge previous models and demonstrate that even in the absence of major specific interaction forces, virtually all tissue-resident cells are invariably in physical contact with, or close proximity to, mesenchymal reticular and sinusoidal endothelial cells. We further show that basic structural features of these stromal components are preserved during ageing., Nature Communications, 9 (1), ISSN:2041-1723

Objective— Low- and high-density lipoproteins (LDL and HDL) must pass the endothelial layer to exert pro- and antiatherogenic activities, respectively, within the vascular wall. However, the rate-limiting factors that mediate transendothelial transport of lipoproteins are yet little known. Therefore, we performed a high-throughput screen with kinase drug inhibitors to identify modulators of transendothelial LDL and HDL transport. Approach and Results— Microscopy-based high-content screening was performed by incubating human aortic endothelial cells with 141 kinase-inhibiting drugs and fluorescent-labeled LDL or HDL. Inhibitors of vascular endothelial growth factor (VEGF) receptors (VEGFR) significantly decreased the uptake of HDL but not LDL. Silencing of VEGF receptor 2 significantly decreased cellular binding, association, and transendothelial transport of 125 I-HDL but not 125 I-LDL. RNA interference with VEGF receptor 1 or VEGF receptor 3 had no effect. Binding, uptake, and transport of HDL but not LDL were strongly reduced in the absence of VEGF-A from the cell culture medium and were restored by the addition of VEGF-A. The restoring effect of VEGF-A on endothelial binding, uptake, and transport of HDL was abrogated by pharmacological inhibition of phosphatidyl-inositol 3 kinase/protein kinase B or p38 mitogen-activated protein kinase, as well as silencing of scavenger receptor BI. Moreover, the presence of VEGF-A was found to be a prerequisite for the localization of scavenger receptor BI in the plasma membrane of endothelial cells. Conclusions— The identification of VEGF as a regulatory factor of transendothelial transport of HDL but not LDL supports the concept that the endothelium is a specific and, hence, druggable barrier for the entry of lipoproteins into the vascular wall.

Optical tweezers are widely used to measure molecular forces in biology. Such measurements are often influenced by a nearby surface that can perturb both the calibration of the tweezers as well as the hydrodynamic forces acting on microspheres to which the biomolecules are attached. In this study, we have used a very stable optical tweezers setup employing a recently developed calibration method (Tolić-Nørrelykke, S. F.; Schäffer, E.; Howard, J.; Pavone, F. S.; Jülicher, F.; Flyvbjerg, H. Rev. Sci. Instrum. 2006, 77 (10), 103101) to determine how the calibration of the tweezers and the forces on the microspheres depend on the height above the surface. We show that the displacement sensitivity of the tweezers is modulated by a standing light wave between the microsphere and the surface. We measured the dependence of the drag coefficient on height and compared it to exact and closed-form solutions to the Navier-Stokes equations. Also, we measured the surface force gradients in different salt solutions and for different surface blocking methods. For a given blocking method, our data suggest that microspheres can experience attractive and/or repulsive forces close to surfaces. For example, a Teflon layer reduces attractive interactions, and the presence of casein can lead to long-range repulsive interactions. These measurements are a prerequisite for the accurate measurement of normal forces with respect to an interface that occur in biological molecules held between surfaces.

We present a dynamical many-body theory of money in which the value of money is a time dependent ``strategic variable'' that is chosen by the individual agents. The value of money in equilibrium is not fixed by the equations, and thus represents a continuous symmetry. The dynamics breaks this continuous symmetry by fixating the value of money at a level which depends on initial conditions. The fluctuations around the equilibrium, for instance in the presence of noise, are governed by the ``Goldstone modes'' associated with the broken symmetry. The idea is illustrated by a simple network model of monopolistic vendors and buyers.

The stochastic dynamics of the damped harmonic oscillator in a heat bath is simulated with an algorithm that is exact for time steps of arbitrary size. Exact analytical results are given for correlation functions and power spectra in the form they acquire when computed from experimental time-lapse recordings. Three applications are discussed: (i) Effects of finite sampling-rate and -time, described exactly here, are similar for other stochastic dynamical systems-e.g. motile micro-organisms and their time-lapse recorded trajectories. (ii) The same statistics is satisfied by any experimental system to the extent it is interpreted as a damped harmonic oscillator at finite temperature-such as an AFM cantilever. (iii) Three other models of fundamental interest are limiting cases of the damped harmonic oscillator at finite temperature; it consequently bridges their differences and describes effects of finite sampling rate and sampling time for these models as well. Finally, we give a brief discussion of nondimensionalization., Comment: 12 pages, 8 figures

Optical tweezers and AFM cantilevers are often calibrated by fitting their experimental powerspectra of Brownian motion. We demonstrate here that if this is done with typical weighted least-squares methods the result is a bias of relative size between -2/n and +1/n on the value of the fitted diffusion coefficient. Here n is the number of power-spectra averaged over, so typical calibrations contain 10-20% bias. Both the sign and the size of the bias depends on the weighting scheme applied. Hence, so do length-scale calibrations based on the diffusion coefficient. The fitted value for the characteristic frequency is not affected by this bias. For the AFM then, force measurements are not affected provided an independent length-scale calibration is available. For optical-tweezers there is no such luck, since the spring constant is found as the ratio of the characteristic frequency and the diffusion coefficient. We give analytical results for the weight-dependent bias for the wide class of systems whose dynamics is described by a linear (integro-)differential equation with additive noise, white or colored. Examples are optical tweezers with hydrodynamic self-interaction and aliasing, calibration of Ornstein-Uhlenbeck models in finance, models for cell-migration in biology, etc. Because the bias takes the form of a simple multiplicative factor on the fitted amplitude (e.g. the diffusion coefficient) it is straightforward to remove, and the user will need minimal modifications to his or her favorite least-square fitting programs. Results are demonstrated and illustrated using synthetic data, so we can compare fits with known true values. We also fit some commonly occurring power spectra once-and-for-all in the sense that we give their parameter values and associated error-bars as explicit functions of experimental power-spectral values., Comment: 20 pages, 10 figures

A simple model economy with interacting producers and consumers is introduced. When driven by extreme dynamics, the model self-organizes not to an attractor state, but to an asymptote, on which the economy has a constant rate of deflation, is critical, and exhibits avalanches of activity with power-law distributed sizes. This example demonstrates that self-organized critical behavior occurs in a larger class of systems than so far considered: systems not driven to an attractive fixed point, but, e.g., an asymptote, may also display self-organized criticality.

Cells derive their structural properties from a complex and active arrangement of stiff polymers. How those proteins interact to give rise to the cell’s diverse characteristics remains a key problem in biological physics.

Why is ``worthless'' fiat money generally accepted as payment for goods and services? In equilibrium theory, the value of money is generally not determined: the number of equations is one less than the number of unknowns, so only relative prices are determined. In the language of mathematics, the equations are ``homogeneous of order one''. Using the language of physics, this represents a continuous ``Goldstone'' symmetry. However, the continuous symmetry is often broken by the dynamics of the system, thus fixing the value of the otherwise undetermined variable. In economics, the value of money is a strategic variable which each agent must determine at each transaction by estimating the effect of future interactions with other agents. This idea is illustrated by a simple network model of monopolistic vendors and buyers, with bounded rationality. We submit that dynamical, spontaneous symmetry breaking is the fundamental principle for fixing the value of money. Perhaps the continuous symmetry representing the lack of restoring force is also the fundamental reason for large fluctuations in stock markets., Comment: 7 pages, 3 figures

Do individual cells have a search strategy when their target is outside their range of detection? Does this strategy change when a high density of targets is encountered?To answer these questions, we observed single, well-isolated cells of the social amoeba Dictyostelium as they forage for bacteria on a flat surface. Time-lapse movies of this predator-prey system were recorded and analyzed. By varying the concentration of the food source over several orders of magnitude the dynamics of the amoebae as they responded to their environment could be studied.At low bacterial density the amoebae scooped up the bacteria as they passed over them without any detectable change in motion. At higher bacterial density the amoebae slowed down, picking up essentially all bacteria encountered, and were found to change their long-timescale behavior from an unbiased random walk to a self-avoiding random walk. This way the amoebae avoids searching for food in already depleted regions. A single amoeba typically ingested 250 bacteria before pausing for 15 min to divide.