Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images.

Microscopy-based spatially resolved omic methods are transforming the life sciences. However, these methods rely on high numerical aperture objectives and cannot resolve crowded molecular targets, limiting the amount of extractable biological information. To overcome these limitations, here we develop Deconwolf, an open-source, user-friendly software for high-performance deconvolution of widefield fluorescence microscopy images, which efficiently runs on laptop computers. Deconwolf enables accurate quantification of crowded diffraction limited fluorescence dots in DNA and RNA fluorescence in situ hybridization images and allows robust detection of individual transcripts in tissue sections imaged with ×20 air objectives. Deconvolution of in situ spatial transcriptomics images with Deconwolf increased the number of transcripts identified more than threefold, while the application of Deconwolf to images obtained by fluorescence in situ sequencing of barcoded Oligopaint probes drastically improved chromosome tracing. Deconwolf greatly facilitates the use of deconvolution in many bioimaging applications.

Separation of transcriptional repressor and activator functions in Drosophila HDAC3.

The histone deacetylase HDAC3 is associated with the NCoR/SMRT co-repressor complex, and its canonical function is in transcriptional repression, but it can also activate transcription. Here, we show that the repressor and activator functions of HDAC3 can be genetically separated in Drosophila. A lysine substitution in the N terminus (K26A) disrupts its catalytic activity and activator function, whereas a combination of substitutions (HEBI) abrogating the interaction with SMRTER enhances repressor activity beyond wild type in the early embryo. We conclude that the crucial functions of HDAC3 in embryo development involve catalytic-dependent gene activation and non-enzymatic repression by several mechanisms, including tethering of loci to the nuclear periphery.

Light scattering in fibrous media with different degrees of in-plane fiber alignment.

Fiber orientation is an important structural property in paper and other fibrous materials. In this study we explore the relation between light scattering and in-plane fiber orientation in paper sheets. Light diffusion from a focused light source is simulated using a Monte Carlo technique where parameters describing the paper micro-structure were determined from 3D x-ray computed tomography images. Measurements and simulations on both spatially resolved reflectance and transmittance light scattering patterns show an elliptical shape where the main axis is aligned towards the fiber orientation. Good qualitative agreement was found at low intensities and the results indicate that fiber orientation in thin fiber-based materials can be determined using spatially resolved reflectance or transmittance.

Lateral interactions in brush layers of bottle-brush polymers.

We used isotension-ensemble Monte Carlo simulations to study the properties of brush layers of bottle-brush polymers under lateral compression. The polymers were represented by a freely jointed hard-bead model with one side chain grafted to each bead of the main chain, and we considered variations in side-chain length and bead size. Brush properties, including brush height and surface pressure, were analyzed in the context of a generalized box model. The surface pressure was found to have a steeper dependence on the grafting density than predicted by classical theories of polymer brushes. This discrepancy could be traced to the equation of state of the polymer fluid composing the brush, which was found to be more reminiscent of the concentrated regime than of the semidilute conditions normally expected in polymer brushes. The conformational properties of individual polymer molecules were found to be insensitive to lateral compression; in particular, the side-chain end-to-end distance remained essentially constant.

Mechanisms of acceleration and retardation of water dynamics by ions.

There are fundamental and not yet fully resolved questions concerning the impact of solutes, ions in particular, on the structure and dynamics of water, which can be formulated as follows: Are the effects of ions local or long-ranged? Is the action of cations and anions on water cooperative or not? Here, we investigate how the reorientation and hydrogen-bond dynamics of water are affected by ions in dilute and concentrated aqueous salt solutions. By combining simulations and analytic modeling, we first show that ions have a short-ranged influence on the reorientation of individual water molecules and that depending on their interaction strength with water, they may accelerate or slow down water dynamics. A simple additive picture combining the effects of the cations and anions is found to provide a good description in dilute solutions. In concentrated solutions, we show that the average water reorientation time ceases to scale linearly with salt concentration due to overlapping hydration shells and structural rearrangements which reduce the translational displacements induced by hydrogen-bond switches and increase the solution viscosity. This effect is not ion-specific and explains why all concentrated salt solutions slow down water dynamics. Our picture, which is demonstrated to be robust vis-a-vis a change in the force-field, reconciles the seemingly contradictory experimental results obtained by ultrafast infrared and NMR spectroscopies, and suggests that there are no long-ranged cooperative ion effects on the dynamics of individual water molecules in dilute solutions.

Spreading and brush formation by end-grafted bottle-brush polymers with adsorbing side chains.

We investigate structural and thermodynamic properties of surface-grafted layers of model "bottle-brush" polymers by Monte Carlo simulation. The polymers consist of a longer main chain densely grafted with shorter side chains, of which the latter have some degree of affinity to the surface. Our focus is on the effect of the side-chain surface affinity on the brush properties, which we study in terms of compression isotherms spanning a broad range of grafting densities. For low grafting densities, side-chain adsorption causes the polymers to spread on the surface. As the grafting density is increased, the layer goes through a "pancake-to-brush" transition to form a brush with the main chains aligned perpendicular to the surface. We find that side-chain adsorption is decisive for the structure of dilute layers and in the transition region but has little influence on the properties of dense brushes. The close relation between compression and adsorption isotherms is discussed, and the implications of side-chain adsorption for the ability of the polymer to form a dense brush are investigated. This analysis suggests that side-chain surface affinity alone will not give rise to "brush of bottle-brushes" layers by adsorption of polymers from solution, in agreement with recent experimental results.

Postprocessing method for reducing phase effects in reconstructed microcomputed-tomography data.

With increased resolution in x-ray computed tomography, refraction adds increasingly to the attenuation signal. Though potentially beneficial, the artifacts caused by refraction often need to be removed from the image. In this paper, we propose a postprocessing method, based on deconvolution, that is able to remove these artifacts after conventional reconstruction. This method poses two advantages over existing projection-based (preprocessing) phase-retrieval or phase-removal algorithms. First, evaluation of the parameters can be done very quickly, improving the overall speed of the method. Second, postprocessing methods can be applied when projection data is not available, which occurs in several commercial systems with closed software or when projection data has been deleted. It is shown that the proposed method performs comparably to state-of-the-art methods in terms of image quality.

Counterion condensation in short cationic peptides: limiting mobilities beyond the Onsager-Fuoss theory.

We investigated the effect of the background electrolyte (BGE) anions on the electrophoretic mobilities of the cationic amino acids arginine and lysine and the polycationic peptides tetraarginine, tetralysine, nonaarginine, and nonalysine. BGEs composed of sodium chloride, sodium propane-1,3-disulfonate, and sodium sulfate were used. For the amino acids, determination of the limiting mobility by extrapolation, using the Onsager-Fuoss (OF) theory expression, yielded consistent estimates. For the peptides, however, the estimates of the limiting mobilities were found to spuriously depend on the BGE salt. This paradox was resolved using molecular modeling. Simulations, on all-atom as well as coarse-grained levels, show that significant counterion condensation, an effect not accounted for in OF theory, occurs for the tetra- and nonapeptides, even for low BGE concentrations. Including this effect in the quantitative estimation of the BGE effect on mobility removed the discrepancy between the estimated limiting mobilities in different salts. The counterion condensation was found to be mainly due to electrostatic interactions, with specific ion effects playing a secondary role. Therefore, the conclusions are likely to be generalizable to other analytes with a similar density of charged groups and OF theory is expected to fail in a predictable way for such analytes.

Overcharging in biological systems: reversal of electrophoretic mobility of aqueous polyaspartate by multivalent cations.

Charge reversal as an extreme case of charge compensation is directly observed by capillary electrophoresis for a negatively charged peptide in aqueous solutions of trivalent cations. Atomistic and coarse-grained simulations provide molecular interpretation of this effect showing that it is largely of electrostatic origin with a minor contribution of chemical specificity of the salt ions.

Solvation and ion-pairing properties of the aqueous sulfate anion: explicit versus effective electronic polarization.

We assessed the relative merits of two approaches for including polarization effects in classical force fields for the sulfate anion. One of the approaches is the explicit shell model for atomic polarization and the other is an implicit dielectric continuum representation of the electronic polarization, wherein the polarizability density is spatially uniform. Both the solvation and ion association properties of sulfate were considered. We carried out an ab initio molecular dynamics simulation for a single sulfate anion in aqueous solution to obtain a benchmark for the solvation structure. For the ion-pairing properties, the models were compared to experimental thermodynamic data through Kirkwood-Buff theory, which relates the integrals of the pair correlation functions to measurable properties. While deficiencies were found for both of the approaches, the continuum polarization model was not systematically worse than the shell model. The shell model was found to give a more structured solution than the continuum polarization model, both with respect to solvation and ion pairing.

Simultaneous visualization of DNA loci in single cells by combinatorial multi-color iFISH.

Single-molecule DNA fluorescence in situ hybridization (FISH) techniques enable studying the three-dimensional (3D) organization of the genome at the single cell level. However, there is a major unmet need for open access, high quality, curated and reproducible DNA FISH datasets. Here, we describe a dataset obtained by applying our recently developed iFISH method to simultaneously visualize 16 small (size range: 62-73 kilobases, kb) DNA loci evenly spaced on chromosome 2 in human cells, in a single round of hybridization. We show how combinatorial color coding can be used to precisely localize multiple loci in 3D within single cells, and how inter-locus distances scale inversely with chromosome contact frequencies determined by high-throughput chromosome conformation capture (Hi-C). We provide raw images and 3D coordinates for nearly 10,000 FISH dots. Our dataset provides a free resource that can facilitate studies of 3D genome organization in single cells and can be used to develop automatic FISH analysis algorithms.

FRET-FISH probes chromatin compaction at individual genomic loci in single cells.

Chromatin compaction is a key biophysical property that influences multiple DNA transactions. Lack of chromatin accessibility is frequently used as proxy for chromatin compaction. However, we currently lack tools for directly probing chromatin compaction at individual genomic loci. To fill this gap, here we present FRET-FISH, a method combining fluorescence resonance energy transfer (FRET) with DNA fluorescence in situ hybridization (FISH) to probe chromatin compaction at select loci in single cells. We first validate FRET-FISH by comparing it with ATAC-seq, demonstrating that local compaction and accessibility are strongly correlated. FRET-FISH also detects expected differences in compaction upon treatment with drugs perturbing global chromatin condensation. We then leverage FRET-FISH to study local chromatin compaction on the active and inactive X chromosome, along the nuclear radius, in different cell cycle phases, and during increasing passage number. FRET-FISH is a robust tool for probing local chromatin compaction in single cells.

piRNAs initiate transcriptional silencing of spermatogenic genes during C. elegans germline development.

Eukaryotic genomes harbor invading transposable elements that are silenced by PIWI-interacting RNAs (piRNAs) to maintain genome integrity in animal germ cells. However, whether piRNAs also regulate endogenous gene expression programs remains unclear. Here, we show that C. elegans piRNAs trigger the transcriptional silencing of hundreds of spermatogenic genes during spermatogenesis, promoting sperm differentiation and function. This silencing signal requires piRNA-dependent small RNA biogenesis and loading into downstream nuclear effectors, which correlates with the dynamic reorganization of two distinct perinuclear biomolecular condensates present in germ cells. In addition, the silencing capacity of piRNAs is temporally counteracted by the Argonaute CSR-1, which targets and licenses spermatogenic gene transcription. The spatial and temporal overlap between these opposing small RNA pathways contributes to setting up the timing of the spermatogenic differentiation program. Thus, our work identifies a prominent role for piRNAs as direct regulators of endogenous transcriptional programs during germline development and gamete differentiation.

An atlas of endogenous DNA double-strand breaks arising during human neural cell fate determination.

Endogenous DNA double-strand breaks (DSBs) occurring in neural cells have been implicated in the pathogenesis of neurodevelopmental disorders (NDDs). Currently, a genomic map of endogenous DSBs arising during human neurogenesis is missing. Here, we applied in-suspension Breaks Labeling In Situ and Sequencing (sBLISS), RNA-Seq, and Hi-C to chart the genomic landscape of DSBs and relate it to gene expression and genome architecture in 2D cultures of human neuroepithelial stem cells (NES), neural progenitor cells (NPC), and post-mitotic neural cells (NEU). Endogenous DSBs were enriched at the promoter and along the gene body of transcriptionally active genes, at the borders of topologically associating domains (TADs), and around chromatin loop anchors. NDD risk genes harbored significantly more DSBs in comparison to other protein-coding genes, especially in NEU cells. We provide sBLISS, RNA-Seq, and Hi-C datasets for each differentiation stage, and all the scripts needed to reproduce our analyses. Our datasets and tools represent a unique resource that can be harnessed to investigate the role of genome fragility in the pathogenesis of NDDs.

The protonation state of small carboxylic acids at the water surface from photoelectron spectroscopy.

We report highly surface sensitive core-level photoelectron spectra of small carboxylic acids (formic, acetic and butyric acid) and their respective carboxylate conjugate base forms (formate, acetate and butyrate) in aqueous solution. The relative surface propensity of the carboxylic acids and carboxylates is obtained by monitoring their respective C1s signal intensities from a solution in which their bulk concentrations are equal. All the acids are found to be enriched at the surface relative to the corresponding carboxylates. By monitoring the PE signals of acetic acid and acetate as a function of total concentration, we find that the protonation of acetic acid is nearly complete in the interface layer. This is in agreement with literature surface tension data, from which it is inferred that the acids are enriched at the surface while (sodium) formate and acetate, but not butyrate, are depleted. For butyric acid, we conclude that the carboxylate form co-exists with the acid in the interface layer. The free energy cost of replacing an adsorbed butyric acid molecule with a butyrate ion at 1.0 M concentration is estimated to be >5 kJ mol(-1). By comparing concentration dependent surface excess data with the evolution of the corresponding photoemission signals it is furthermore possible to draw conclusions about how the distribution of molecules that contribute to the excess is altered with bulk concentration.

The influence of concentration on the molecular surface structure of simple and mixed aqueous electrolytes.

We investigate various mechanisms contributing to the surface ion distributions in simple and mixed aqueous alkali-halide solutions depending on the total salt concentration, using a combination of photoelectron spectroscopy and molecular dynamics simulations. In simple solutions, the surface enhancement of large polarizable anions is reduced with increasing concentration. In the case of a NaBr/NaCl mixed aqueous solution, with bromide as the minority component, the situation is more complex. While the total anion/cation charge separation is similarly reduced with increasing salt content, this alone does not uniquely determine the ion distribution due to the co-existence of two different anions, Br(-) and Cl(-). We show that bromide is selectively surface enhanced at higher concentrations, despite the fact that the total anion surface enhancement is reduced. This phenomenon, which can be viewed as "salting out" of bromide by NaCl might have consequences for our understanding of the surface structure of mixed aqueous solutions subjected to concentration increase due to dehydration, such as seawater-born aerosols.

GPSeq reveals the radial organization of chromatin in the cell nucleus.

With the exception of lamina-associated domains, the radial organization of chromatin in mammalian cells remains largely unexplored. Here we describe genomic loci positioning by sequencing (GPSeq), a genome-wide method for inferring distances to the nuclear lamina all along the nuclear radius. GPSeq relies on gradual restriction digestion of chromatin from the nuclear lamina toward the nucleus center, followed by sequencing of the generated cut sites. Using GPSeq, we mapped the radial organization of the human genome at 100-kb resolution, which revealed radial patterns of genomic and epigenomic features and gene expression, as well as A and B subcompartments. By combining radial information with chromosome contact frequencies measured by Hi-C, we substantially improved the accuracy of whole-genome structure modeling. Finally, we charted the radial topography of DNA double-strand breaks, germline variants and cancer mutations and found that they have distinctive radial arrangements in A and B subcompartments. We conclude that GPSeq can reveal fundamental aspects of genome architecture.

iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture.

DNA fluorescence in situ hybridization (DNA FISH) is a powerful method to study chromosomal organization in single cells. At present, there is a lack of free resources of DNA FISH probes and probe design tools which can be readily applied. Here, we describe iFISH, an open-source repository currently comprising 380 DNA FISH probes targeting multiple loci on the human autosomes and chromosome X, as well as a genome-wide database of optimally designed oligonucleotides and a freely accessible web interface ( http://ifish4u.org ) that can be used to design DNA FISH probes. We individually validate 153 probes and take advantage of our probe repository to quantify the extent of intermingling between multiple heterologous chromosome pairs, showing a much higher extent of intermingling in human embryonic stem cells compared to fibroblasts. In conclusion, iFISH is a versatile and expandable resource, which can greatly facilitate the use of DNA FISH in research and diagnostics.

Ion correlation forces between uncharged dielectric walls.

The interaction pressure between two uncharged planar walls immersed in various electrolyte solutions containing mono- and/or divalent ions is investigated. The solution is treated as a primitive model electrolyte, and the wall surfaces constitute dielectric discontinuities. Ionic image charge and ion-wall dispersion interactions are included. The interaction parameters are appropriate for hydrocarbon (polystyrene)/water interfaces, and the electrolyte concentrations considered lie between 0.250M and 1.00M. The anisotropic hypernetted chain method is used to self-consistently calculate the ion density profiles and the ion-ion correlation functions in the inhomogeneous electrolyte. Thereby, the effects of image charge interactions and dispersion interactions on the pressure and the electrolyte structure are included in a fully consistent manner. The explicit consideration of correlations between the ions in the presence of image charges ensures that the screening of the zero-frequency van der Waals interaction is taken into account. Of special interest are the effects of asymmetries between anions and cations with respect to valency and/or dispersion interaction with the walls. Such asymmetries create an electric double layer in the electrolyte outside each electroneutral surface. This causes the wall-wall interaction for large surface separations to be similar to the interaction between charged surfaces. For intermediate separations, around 1-2 nm, a substantial repulsive peak appears in the ionic pressure. In some cases the repulsion is larger than the van der Waals attraction between the walls, which implies that there is a repulsive barrier in the total pressure despite that the surfaces are uncharged. The strongest repulsion is found for 2:1 electrolytes where the monovalent anions interact strongly with the walls via dispersion forces. In general, ion-wall dispersion forces acting on ions of lower valency have a much greater effect than equally strong dispersion forces acting on ions of higher valency. This is mainly due to the more strongly repulsive image charge forces on ions of higher valency that counteract the attractive dispersion forces. Effects of confinement on the ion-ion correlations also contribute to this difference. For all electrolytes the interaction pressure from the ions is attractive for small surface separations. The main cause is a depletion of ions between the walls from the self-image repulsion and confinement effects. For totally symmetric electrolytes the attractive pressure extends to large separations in most cases.

An Application-Directed, Versatile DNA FISH Platform for Research and Diagnostics.

DNA fluorescence in situ hybridization (DNA FISH) has emerged as a powerful microscopy technique that allows a unique view into the composition and arrangement of the genetic material in its natural context-be it the cell nucleus in interphase, or chromosomes in metaphase spreads. The core principle of DNA FISH is the ability of fluorescently labeled DNA probes (either double- or single-stranded DNA fragments) to bind to their complementary sequences in situ in cells or tissues, revealing the location of their target as fluorescence signals detectable with a fluorescence microscope. Numerous variants and improvements of the original DNA FISH method as well as a vast repertoire of applications have been described since its inception more than 4 decades ago. In recent years, the development of many new fluorescent dyes together with drastic advancements in methods for probe generation (Boyle et al., Chromosome Res 19:901-909, 2011; Beliveau et al., Proc Natl Acad Sci U S A 109:21301-21306, 2012; Bienko et al., Nat Methods 10:122-124, 2012), as well as improvements in the resolution of microscopy technologies, have boosted the number of DNA FISH applications, particularly in the field of genome architecture (Markaki et al., Bioessays 34:412-426, 2012; Beliveau et al., Nat Commun 6:7147, 2015). However, despite these remarkable steps forward, choosing which type of DNA FISH sample preparation protocol, probe design, hybridization procedure, and detection method is best suited for a given application remains still challenging for many research labs, preventing a more widespread use of this powerful technology. Here, we present a comprehensive platform to help researchers choose which DNA FISH protocol is most suitable for their particular application. In addition, we describe computational pipelines that can be implemented for efficient DNA FISH probe design and for signal quantification. Our goal is to make DNA FISH a versatile and streamlined technique that can be easily implemented by both research and diagnostic labs.