Homozygous single nucleotide duplication of SLC38A8 in autosomal recessive foveal hypoplasia: The first Japanese case report.

PURPOSE: To characterize the clinical and genetic features of a Japanese male patient with foveal hypoplasia caused by a homozygous single nucleotide duplication in the SLC38A8 gene. METHODS: We performed a comprehensive ophthalmic examination including full-field electroretinography (FF-ERG) and pattern-reversal visual evoked potentials (PR-VEPs). Whole-exome sequencing (WES) was performed to identify the disease-causing variant; Sanger sequencing was used for confirmation. RESULTS: In the WES analysis, a homozygous single nucleotide duplication (c.995dupG; p.Trp333MetfsTer35) was identified in SLC38A8 of the patient. His unaffected mother carried the variant heterozygously. The patient exhibited hyperopia, congenital nystagmus, low visual acuity, and grade 4 foveal hypoplasia. Slit-lamp examination revealed mild posterior embryotoxon and goniodysgenesis. Fundus examination revealed the absence of foveal hyperpigmentation and foveal avascularity, but there were no retinal degenerative lesions. In the FF-ERG, the amplitudes of rod ERG, standard-flash, and bright-flash ERG were within the normal range; cone-mediated responses also showed nearly normal amplitudes. The PR-VEP findings revealed delayed P100 latencies and decreased amplitudes of the P100 components, but no chiasmal misrouting. CONCLUSIONS: This report is the first report on the clinical and genetic characteristics of SLC38A8-associated foveal hypoplasia in the Japanese population. This is also the first report of normal rod- and cone-mediated responses in a patient with this disorder.

Quantitative bridging between full-atomistic and bead-spring models for polybutadiene and poly(butadiene-styrene) copolymers.

Despite lots of attempts on the bridging between full-atomistic and coarse-grained models for polymers, a practical methodology has not been established yet. One of the problems is computation costs for the determination of spatial and temporal conversion parameters, which are ideally obtained for the long chain limit. In this study, we propose a practical, yet quantitative, bridging method utilizing the simulation results for rather short chains. We performed full-atomistic simulations for polybutadiene and some poly(butadiene-styrene) copolymers in the melt state by varying the number of repeating units as 20, 30, and 40. We attempted to construct corresponding coarse-grained models for such systems. We employed the Kremer-Grest type bead-spring chains with bending rigidity. The stiffness parameter of coarse-grained models and the spatial conversion factor between the full-atomistic and coarse-grained models were obtained according to the conformational statistics of polymer chains. Although such a bridging strategy is similar to the earlier studies, we incorporated the molecular weight dependence of the conformational statistics for the first time. By introducing several empirical functions of the conformational statistics for the molecular weight dependence, we attained a rigorous bridging for the conformational statistics. We confirmed that the structural distribution functions of the coarse-grained systems are entirely consistent with the target full-atomistic ones. Owing to the structural conversion parameters thus obtained, we constructed the coarse-grained models that corresponded to the polymers consisting of 200 repeating units and traced the segmental diffusion. The full-atomistic simulations were also performed from the initial configurations created from the equilibrated coarse-grained models via the back-mapping scheme. From the comparison of the mean-square-displacement of the segments positioned at the middle of the chain, we obtained the temporal conversion factors.

Conjunctival Chemosis Caused by Exposure of the Lacrimal Caruncle: A Case Report.

An 84-year-old woman presented with a 3-month history of conjunctival chemosis in the left eye. At the first examination, the chemosis neighbored the lacrimal caruncle and was localized in the inferomedial region of the conjunctiva. During eyelid closure, only the left lacrimal caruncle was exposed. One month later, the chemosis further extended to the inferolateral region. We debulked the lacrimal caruncle to prevent the exposure of the caruncle. One month after the surgery, conjunctival chemosis had resolved completely. At the postoperative 6-month follow-up, the patient showed no recurrence of chemosis.

Spatio-temporal hierarchy in the dynamics of a minimalist protein model.

A method for time series analysis of molecular dynamics simulation of a protein is presented. In this approach, wavelet analysis and principal component analysis are combined to decompose the spatio-temporal protein dynamics into contributions from a hierarchy of different time and space scales. Unlike the conventional Fourier-based approaches, the time-localized wavelet basis captures the vibrational energy transfers among the collective motions of proteins. As an illustrative vehicle, we have applied our method to a coarse-grained minimalist protein model. During the folding and unfolding transitions of the protein, vibrational energy transfers between the fast and slow time scales were observed among the large-amplitude collective coordinates while the other small-amplitude motions are regarded as thermal noise. Analysis employing a Gaussian-based measure revealed that the time scales of the energy redistribution in the subspace spanned by such large-amplitude collective coordinates are slow compared to the other small-amplitude coordinates. Future prospects of the method are discussed in detail.

Theoretical model for cell migration with gradient sensing and shape deformation.

Amoeboid cells take various shapes during migration, depending on the cell type and its environment. Deformability of the cell shape can then affect the migrating behavior. In this article, we introduce a theoretical model of chemotactic cell migration with elliptical shape deformation. Based on the model, we calculate the stationary distributions of the migration directions analytically. As a result, we find that the distributions show different characteristics depending on the difference in the interdependence of the internal polarity, cell morphology and gradient sensing.

Long-term observation of fluorescence of free single molecules to explore protein-folding energy landscapes.

A method was developed to detect fluorescence intensity signals from single molecules diffusing freely in a capillary cell. A unique optical system based on a spherical mirror was designed to enable quantitative detection of the fluorescence intensity. Furthermore, "flow-and-stop" control of the sample can extend the observation time of single molecules to several seconds, which is more than 1000 times longer than the observation time available using a typical confocal method. We used this method to scrutinize the fluorescence time series of the labeled cytochrome c in the unfolded state. Time series analyses of the trajectories based on local equilibrium state analysis revealed dynamically differing substates on a millisecond time scale. This system presents a new avenue for experimental characterization of the protein-folding energy landscape.

Directional sensing of deformed cells under faint gradients.

We consider the physical limit of the directional sensing ability of living cells, as in chemotaxis, under a low concentration and shallow chemoattractant gradient. Elliptic cells sense the direction, which is a stochastic variable of a characteristic distribution with peaks at directions not necessarily to the gradient. The peak positions depend on the information of the gradient that cells use to infer the direction and also the shape and orientation of cells. Cells of different shapes may use different inference strategies to increase their directional sensing performance.

Extracting the underlying effective free energy landscape from single-molecule time series--local equilibrium states and their network.

We present a new self-consistent procedure to construct a multidimensional effective free energy landscape from a scalar single molecule time series, when single molecules experience the landscape within a given timescale of "observation." The theory is based on a framework we recently developed to extract a set of local equilibrium states (LESs) and their network from a scalar time series, such as distance between dye molecules tagged in a biomolecule. We scrutinize the appropriateness of the assumptions of local equilibration and local detailed balance among LESs at the single molecule level within the given timescale, rather than postulating them a priori. The self-consistent procedure in this article incorporates the effect of local correlation of the system dynamics inside potential basins, and the effect of finiteness of the sampled data points in assigning the boundary between different LESs. We propose a new simple scheme to assign the dimensionality of the energy landscape from a single molecule time series. We also address the question of what the molecules actually "feel" from the underlying landscape at the single molecule level.

Construction of effective free energy landscape from single-molecule time series.

A scheme for extracting an effective free energy landscape from single-molecule time series is presented. This procedure uniquely identifies a non-Gaussian distribution of the observable associated with each local equilibrium state (LES). Both the number of LESs and the shape of the non-Gaussian distributions depend on the time scale of observation. By assessing how often the system visits and resides in a chosen LES and escapes from one LES to another (with checking whether the local detailed balance is satisfied), our scheme naturally leads to an effective free energy landscape whose topography depends on in which time scale the system experiences the underlying landscape. For example, two metastable states are unified as one if the time scale of observation is longer than the escape time scale for which the system can visit mutually these two states. As an illustrative example, we present the application of extracting the effective free energy landscapes from time series of the end-to-end distance of a three-color, 46-bead model protein. It indicates that the time scales to attain the local equilibrium tend to be longer in the unfolded state than those in the compact collapsed state.

Topographical complexity of multidimensional energy landscapes.

A scheme for visualizing and quantifying the complexity of multidimensional energy landscapes and multiple pathways is presented employing principal component-based disconnectivity graphs and the Shannon entropy of relative "sizes" of superbasins. The principal component-based disconnectivity graphs incorporate a metric relationship between the stationary points of the system, which enable us to capture not only the actual assignment of the superbasins but also the size of each superbasin in the multidimensional configuration space. The landscape complexity measure quantifies the degree of topographical complexity of a multidimensional energy landscape and tells us at which energy regime branching of the main path becomes significant, making the system more likely to be kinetically trapped in local minima. The path complexity measure quantifies the difficulty encountered by the system to reach a connected local minimum by the path in question, implying that the more significant the branching points along the path the more difficult it is to end up in the desired local minimum. As an illustrative example, we apply this analysis to two kinds of small model protein systems exhibiting a highly frustrated and an ideal funnel-like energy landscape.