Chromatin decondensation and nuclear softening accompany Nanog downregulation in embryonic stem cells.

The interplay between epigenetic modification and chromatin compaction is implicated in the regulation of gene expression, and it comprises one of the most fascinating frontiers in cell biology. Although a complete picture is still lacking, it is generally accepted that the differentiation of embryonic stem (ES) cells is accompanied by a selective condensation into heterochromatin with concomitant gene silencing, leaving access only to lineage-specific genes in the euchromatin. ES cells have been reported to have less condensed chromatin, as they are capable of differentiating into any cell type. However, pluripotency itself-even prior to differentiation-is a split state comprising a naïve state and a state in which ES cells prime for differentiation. Here, we show that naïve ES cells decondense their chromatin in the course of downregulating the pluripotency marker Nanog before they initiate lineage commitment. We used fluorescence recovery after photobleaching, and histone modification analysis paired with a novel, to our knowledge, optical stretching method, to show that ES cells in the naïve state have a significantly stiffer nucleus that is coupled to a globally more condensed chromatin state. We link this biophysical phenotype to coinciding epigenetic differences, including histone methylation, and show a strong correlation of chromatin condensation and nuclear stiffness with the expression of Nanog. Besides having implications for transcriptional regulation and embryonic cell sorting and suggesting a putative mechanosensing mechanism, the physical differences point to a system-level regulatory role of chromatin in maintaining pluripotency in embryonic development.

Comparison of stresses on homogeneous spheroids in the optical stretcher computed with geometrical optics and generalized Lorenz-Mie theory.

We present two electromagnetic frameworks to compare the surface stresses on spheroidal particles in the optical stretcher (a dual-beam laser trap that can be used to capture and deform biological cells). The first model is based on geometrical optics (GO) and limited in its applicability to particles that are much greater than the incident wavelength. The second framework is more sophisticated and hinges on the generalized Lorenz-Mie theory (GLMT). Despite the difference in complexity between both theories, the stress profiles computed with GO and GLMT are in good agreement with each other (relative errors are on the order of 1-10%). Both models predict a diminishing of the stresses for larger wavelengths and a strong increase of the stresses for shorter laser-cell distances. Results indicate that surface stresses on a spheroid with an aspect ratio of 1.2 hardly differ from the stresses on a sphere of similar size. Knowledge of the surface stresses and whether or not they redistribute during the stretching process is of crucial importance in real-time applications of the stretcher that aim to discern the viscoelastic properties of cells for purposes of cell characterization, sorting, and medical diagnostics.

Exact analytical expansion of an off-axis Gaussian laser beam using the translation theorems for the vector spherical harmonics.

The interaction of a Gaussian laser beam with a particle that is located off axis is a fundamental problem encountered across many scientific fields, including biological physics, chemistry, and medicine. For spherical geometries, generalized Lorenz-Mie theory affords a solution of Maxwell's equations for the scattering from such a particle. The solution can be obtained by expanding the laser fields in terms of vector spherical harmonics (VSHs). However, the computation of the VSH expansion coefficients for off-axis beams has proven challenging. In the present study, we provide a very viable, theoretical framework to efficiently compute the sought-after expansion coefficients with high numerical accuracy. We use the existing theory for the expansion of an on-axis laser beam and employ Cruzan's translation theorems [Q. Appl. Math.20, 33 (1962)] for the VSHs to obtain a description for more general off-axis beams. The expansion coefficients for the off-axis laser beam are presented in an analytical form in terms of an infinite series over the underlying translation coefficients. A direct comparison of the electromagnetic fields of such a beam expansion with the original laser fields and with results obtained using numerical quadratures shows excellent agreement (relative errors are on the order of ≲10(-3). In practice, the analytical approach presented in this study has numerous applications, reaching from multiparticle scattering problems in atmospheric physics and climatology to optical trapping, sorting, and sizing techniques.

Physical insight into light scattering by photoreceptor cell nuclei.

A recent study showed that the rod photoreceptor cell nuclei in the retina of nocturnal and diurnal mammals differ considerably in architecture: the location of euchromatin and heterochromatin in the nucleus is interchanged. This inversion has significant implications for the refractive index distribution and the light scattering properties of the nucleus. Here, we extend previous two-dimensional analysis to three dimensions (3D) by using both a numerical finite-difference time-domain and an analytic Mie theory approach. We find that the specific arrangement of the chromatin phases in the nuclear core-shell models employed have little impact on the far-field scattering cross section. However, scattering in the near field, which is the relevant regime inside the retina, shows a significant difference between the two architectures. The "inverted" photoreceptor cell nuclei of nocturnal mammals act as collection lenses, with the lensing effect being much more pronounced in 3D than in two dimensions. This lensing helps to deliver light efficiently to the light-sensing outer segments of the rod photoreceptor cells and thereby improve night vision.

Near- and far-field scattering from arbitrary three-dimensional aggregates of coated spheres using parallel computing.

Many scientific fields--including astronomy, climatology, and biology, among others--require the calculation of the scattered optical fields from multiparticle distributions. In the present study, we combine the established results for the scattering from clusters of homogeneous spheres and from single core-shell particles into a computationally tractable solution that is valid for irregular configurations of nonidentical, coated particles. The presented multiparticle scattering (MPS) model is based on a generalized Lorenz-Mie theory framework and the vector translation theorems for the vector spherical harmonics. We provide the MPS model in both the near and far fields, and for plane-wave and Gaussian beam illumination. A message-passing-interface protocol is used for the computational implementation of the model in a parallel computer program. The computer model is validated by verifying the accuracy of the vector translation theorems utilized in our theoretical methods and by qualitative comparison to existing multiparticle scattering data. We conclude by presenting the scattering profiles from several examples of particle distributions. This MPS model is a practicable method of calculating the optical fields arising in the scattering from particle aggregates and is straightforwardly extensible to arbitrary illumination and to more complex internal-particle structures, such as stratified spheres. Vital applications of this model include the exact computation of forces exerted on irregular objects in optical traps and the simulation of light propagation through biological tissues.

Interaction of Gaussian beam with near-spherical particle: an analytic-numerical approach for assessing scattering and stresses.

We derive a straightforward theoretical method to determine the electromagnetic fields for the incidence of a monochromatic laser beam on a near-spherical dielectric particle. The beam-shape coefficients are obtained from the radial laser fields and expressed as a finite series in a form that has, to our knowledge, not been published before. Our perturbation approach to solve Maxwell's equations in spherical coordinates employs two alternative techniques to match the boundary conditions: an analytic approach for small particles with low eccentricity and an adapted point-matching method for larger spheroids with higher aspect ratios. We present results for the internal and external fields, scattering intensities, and stresses exerted on the particle. While similarly accurate as others, our approach is easily implemented numerically and thus particularly useful in praxis, e.g., for analyzing optical traps, such as the optical stretcher.