Markko Myllys

Nuclear Aggregation of Olfactory Receptor Genes Governs Their Monogenic Expression

Gene positioning and regulation of nuclear architecture are thought to influence gene expression. Here, we show that, in mouse olfactory neurons, silent olfactory receptor (OR) genes from different chromosomes converge in a small number of heterochromatic foci. These foci are OR exclusive and form in a cell-type-specific and differentiation-dependent manner. The aggregation of OR genes is developmentally synchronous with the downregulation of lamin b receptor (LBR) and can be reversed by ectopic expression of LBR in mature olfactory neurons. LBR-induced reorganization of nuclear architecture and disruption of OR aggregates perturbs the singularity of OR transcription and disrupts the targeting specificity of the olfactory neurons. Our observations propose spatial sequestering of heterochromatinized OR family members as a basis of monogenic and monoallelic gene expression.

Soft X-ray tomography of phenotypic switching and the cellular response to antifungal peptoids in Candida albicans

The opportunistic pathogen Candida albicans can undergo phenotypic switching between a benign, unicellular phenotype and an invasive, multicellular form that causes candidiasis. Increasingly, strains of Candida are becoming resistant to antifungal drugs, making the treatment of candidiasis difficult, especially in immunocompromised or critically ill patients. Consequently, there is a pressing need to develop new drugs that circumvent fungal drug-resistance mechanisms. In this work we used soft X-ray tomography to image the subcellular changes that occur as a consequence of both phenotypic switching and of treating C. albicans with antifungal peptoids, a class of candidate therapeutics unaffected by drug resistance mechanisms. Peptoid treatment suppressed formation of the pathogenic hyphal phenotype and resulted in striking changes in cell and organelle morphology, most dramatically in the nucleus and nucleolus, and in the number, size, and location of lipidic bodies. In particular, peptoid treatment was seen to cause the inclusion of lipidic bodies into the nucleus.

Putting molecules in their place.

Each class of microscope is limited to imaging specific aspects of cell structure and/or molecular organization. However, imaging the specimen by complementary microscopes and correlating the data can overcome this limitation. Whilst not a new approach, the field of correlative imaging is currently benefitting from the emergence of new microscope techniques. Here we describe the correlation of cryogenic fluorescence tomography (CFT) with soft X‐ray tomography (SXT). This amalgamation of techniques integrates 3D molecular localization data (CFT) with a high‐resolution, 3D cell reconstruction of the cell (SXT). Cells are imaged in both modalities in a near‐native, cryopreserved state. Here we describe the current state of the art in correlative CFT‐SXT, and discuss the future outlook for this method. J. Cell. Biochem. 115: 209–216, 2014.

Diffusion of Tracer in Altered Tonalite: Experiments and Simulations with Heterogeneous Distribution of Porosity

Numerical time-domain-diffusion simulations were used for studying the diffusion behavior of tracer molecules in rock matrix with homogeneous and heterogeneous porosity. As the heterogeneous sample in these simulations, a 3D tomographic image of altered tonalite was used, in which the mineral components and the pores resolved by X-ray microtomography were represented by their respective intragranular porosities determined previously by the 14C-PMMA method. The apparent diffusion coefficient of a tracer in altered tonalite was determined experimentally, and was then used in the simulations. In the altered tonalite analyzed, inclusion of heterogeneity in the porosity increased the diffusion coefficient by 16 %. Altered and pristine feldspar was the main mineral component in the sample (72 %), and it also provided the dominant contribution to tracer diffusion, explaining alone 52 % of the diffusion coefficient. The large pores resolved by microtomography (6 %) and altered and pristine mica (22 %) gave an equal contribution to the diffusion coefficient. The simulation method applied was also validated by comparing the results to both an analytical and a numerical solution to the diffusion equation in a homogenous medium. In addition, the method was compared to discrete-time random-walk simulations in the case of randomly placed overlapping spheres.

A prospect for computing in porous materials research: Very large fluid flow simulations

Abstract Properties of porous materials, abundant both in nature and industry, have broad influences on societies via, e.g. oil recovery, erosion, and propagation of pollutants. The internal structure of many porous materials involves multiple scales which hinders research on the relation between structure and transport properties: typically laboratory experiments cannot distinguish contributions from individual scales while computer simulations cannot capture multiple scales due to limited capabilities. Thus the question arises how large domain sizes can in fact be simulated with modern computers. This question is here addressed using a realistic test case; it is demonstrated that current computing capabilities allow the direct pore-scale simulation of fluid flow in porous materials using system sizes far beyond what has been previously reported. The achieved system sizes allow the closing of some particular scale gaps in, e.g. soil and petroleum rock research. Specifically, a full steady-state fluid flow simulation in a porous material, represented with an unprecedented resolution for the given sample size, is reported: the simulation is executed on a CPU-based supercomputer and the 3D geometry involves 16,384 3 lattice cells (around 590 billion of them are pore sites). Using half of this sample in a benchmark simulation on a GPU-based system, a sustained computational performance of 1.77 PFLOPS is observed. These advances expose new opportunities in porous materials research. The implementation techniques here utilized are standard except for the tailored high-performance data layouts as well as the indirect addressing scheme with a low memory overhead and the truly asynchronous data communication scheme in the case of CPU and GPU code versions, respectively.

Herpes simplex virus 1 induces egress channels through marginalized host chromatin

Lytic infection with herpes simplex virus type 1 (HSV-1) induces profound modification of the cell nucleus including formation of a viral replication compartment and chromatin marginalization into the nuclear periphery. We used three-dimensional soft X-ray tomography, combined with cryogenic fluorescence, confocal and electron microscopy, to analyse the transformation of peripheral chromatin during HSV-1 infection. Our data showed an increased presence of low-density gaps in the marginalized chromatin at late infection. Advanced data analysis indicated the formation of virus-nucleocapsid-sized (or wider) channels extending through the compacted chromatin of the host. Importantly, confocal and electron microscopy analysis showed that these gaps frequently contained viral nucleocapsids. These results demonstrated that HSV-1 infection induces the formation of channels penetrating the compacted layer of cellular chromatin and allowing for the passage of progeny viruses to the nuclear envelope, their site of nuclear egress.

Chromatin organization regulates viral egress dynamics

Various types of DNA viruses are known to elicit the formation of a large nuclear viral replication compartment and marginalization of the cell chromatin. We used three-dimensional soft x-ray tomography, confocal and electron microscopy, combined with numerical modelling of capsid diffusion to analyse the molecular organization of chromatin in herpes simplex virus 1 infection and its effect on the transport of progeny viral capsids to the nuclear envelope. Our data showed that the formation of the viral replication compartment at late infection resulted in the enrichment of heterochromatin in the nuclear periphery accompanied by the compaction of chromatin. Random walk modelling of herpes simplex virus 1–sized particles in a three-dimensional soft x-ray tomography reconstruction of an infected cell nucleus demonstrated that the peripheral, compacted chromatin restricts viral capsid diffusion, but due to interchromatin channels capsids are able to reach the nuclear envelope, the site of their nuclear egress.

Interface Detection Using a Quenched-Noise Version of the Edwards–Wilkinson Equation

We report here a multipurpose dynamic-interface-based segmentation tool, suitable for segmenting planar, cylindrical, and spherical surfaces in 3D. The method is fast enough to be used conveniently even for large images. Its implementation is straightforward and can be easily realized in many environments. Its memory consumption is low, and the set of parameters is small and easy to understand. The method is based on the Edwards-Wilkinson equation, which is traditionally used to model the equilibrium fluctuations of a propagating interface under the influence of temporally and spatially varying noise. We report here an adaptation of this equation into multidimensional image segmentation, and its efficient discretization.

X-ray microtomography and laser ablation in the analysis of ink distribution in coated paper

A novel method was developed for studying the ink-paper interface and the structural variations of a deposited layer of ink. Combining high-resolution x-ray tomography with laser ablation, the depth profile of ink (toner), i.e., its varying thickness, could be determined in a paper substrate. X-ray tomography was used to produce the 3D structure of paper with about 1 μm spatial resolution. Laser ablation combined with optical imaging was used to produce the 3D structure of the printed layer of ink on top of that paper with about 70 nm depth resolution. Ablation depth was calibrated with an optical profilometer. It can be concluded that a toner layer on a light-weight-coated paper substrate was strongly perturbed by protruding fibers of the base paper. Such fibers together with the surface topography of the base paper seem to be the major factors that control the leveling of toner and its penetration into a thinly coated paper substrate.

Evaluating pulp stiffness from fibre bundles by ultrasound

A non-destructive ultrasonic tester was developed to measure the stiffness of pulp bundles. The mechanical properties of pulp are important when estimating the behaviour of paper under stress. Currently available pulp tests are tedious and alter the fibres structurally and mechanically. The developed tester employs (933 ± 15) kHz tweezer-like ultrasonic transducers and time-of-flight measurement through (9.0 ± 2.5) mm long and (0.8 ± 0.1) mm thick fibre bundles kept at (19.1 ± 0.4) °C and (62 ± 1)% RH. We determined the stiffness of soft wood pulps produced by three kraft pulping modifications: standard kraft pulp, (5.2 ± 0.4) GPa, prehydrolysis kraft pulp, (4.3 ± 0.4) GPa, and alkali extracted prehydrolysis kraft pulp, (3.3 ± 0.4) GPa. Prehydrolysis and alkali extraction processes mainly lowered the hemicellulose content of the pulps, which essentially decreased the fibre-wall stiffness hence impairing the stiffness of the fibre networks. Our results indicate that the method allows ranking of pulps according to their stiffness determined from bundle-like samples taken at an early phase of the papermaking process.