ePURE_JSBML: A Tool for Constructing a Deterministic Model of a Reconstituted Escherichia coli Protein Translation System with a User-Specified Nucleic Acid Sequence.

A protein synthesis system is one of the most important and complex biological networks, which translates DNA-encoded information into specific functions. Here, ePURE_JSBML, a tool for constructing biologically relevant large-scale and detailed computational models based on a reconstituted cell-free protein synthesis system, is presented; the user can specify the mRNA sequence, initial component concentration, and decoding rule. Model construction is based on Systems Biology Markup Language (SBML) using JSBML, a pure Java programming library. The tool generates simulation files, executable with Matlab, that enable a variety of simulation experiments including the synthesis of proteins of a few hundred residues.

Vision With Retrodots and Factors for Declining Visual Function.

Purpose: We investigated decline in the visual function of eyes with retrodots (RDs)-a subtype of cataract. Method: This study included 57 eyes with RD opacity only (mean age 72.3 ± 5.2 years) and 34 eyes with transparent lenses (mean age 71.4 ± 3.7 years). A physician diagnosed lens opacity. Using the Kanazawa Medical University Classification and Grading System, the eyes were classified into the RD-1 (37 eyes, RDs <25% of the 3-mm pupil area) and RD-2 (20 eyes, RDs ≥25% of the 3-mm pupil area) groups. Corrected distance visual acuity, contrast visual acuity, ocular refractive power, lens power, straylight, and backward light-scattering intensity and their relationship with visual function decline and optical characteristics of the eyeball were evaluated. Results: Corrected distance visual acuity was significantly lower in the RD eyes than in controls. Contrast visual acuity decreased significantly in the RD-2 eyes in all environments and in the RD-1 eyes in the evening (EVE) and EVE + glare. Straylight was significantly higher in the RD-2 eyes than in the controls and RD-1 eyes but not different between the RD-1 eyes and controls. The RD-2 eyes were significantly more myopic than the controls and RD-1 eyes. Conclusion: When the opacity of RD eyes is ≥25%, the visual acuity and contrast visual acuity decrease and straylight increases. Furthermore, myopia occurs as the refractive power of the lens increases. Moreover, visual function decline may be due to an increase in the straylight value, which is necessary for determining surgical indications.

SBML Level 3: an extensible format for the exchange and reuse of biological models.

Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction-based models and packages that extend the core with features suited to other model types including constraint-based models, reaction-diffusion models, logical network models, and rule-based models. The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with models. More recently, the rise of multiscale models of whole cells and organs, and new data sources such as single-cell measurements and live imaging, has precipitated new ways of integrating data with models. We provide our perspectives on the challenges presented by these developments and how SBML Level 3 provides the foundation needed to support this evolution.

Visual Function and Functional Decline in Patients With Waterclefts.

Purpose: To investigate visual function in eyes with three subtypes of waterclefts (WCs). Methods: Of patients in Kanazawa Medical University Hospital (2013-2017) and participants of Monzen Eye Study (2013-2016), 77 transparent lenses, mean age 66.7 years, and 70 eyes with only WC opacity of 70 patients, mean age 68.1 years, divided into peripheral-, central-, and total-type WC groups, were analyzed. Opacity was classified by one ophthalmologist using slit-lamp microscopy. Corrected-distance visual acuity (CDVA), contrast visual acuity (CVA), spherical equivalent (SE), astigmatism values, corneal refractive power (CP), axial length (AL), straylight, backward light scattering (BLS), and higher order aberrations (HOA) were measured and lenticular refractive power (LP) was calculated based on the values of AL, CP, and SE. Results: Central-type WC showed significant decrease in CDVA and CVA and increase in straylight compared with control. Total-type WC showed significant decreases in CDVA, CVA, and LP, and increase in straylight, compared with control and peripheral-type WC. Total- and central-type WCs had significantly higher ocular total HOA and total-type WC had significantly higher internal total HOA than control. HOA correlated positively with CDVA (P < 0.001) and straylight (P = 0.020), and CDVA negatively with straylight in eyes with WCs (P = 0.008). Conclusions: Total-type WC was associated with decreased LP, causing hyperopia, decreased CDVA and higher straylight; thus, such lenticular change should be considered for surgery indication. Significant correlations between HOA and both CDVA and straylight suggested increased HOA may decrease visual function in eyes with WCs.

Significance of Data Selection in Deep Learning for Reliable Binding Mode Prediction of Ligands in the Active Site of CYP3A4.

For rational drug design, it is essential to predict the binding mode of protein-ligand complexes. Although various machine learning-based models have been reported that use convolutional neural networks (deep learning) to predict binding modes from three-dimensional structures, there are few detailed reports on how best to construct and use datasets. Here, we examined how different datasets affected the prediction of the binding mode of CYP3A4 by a three-dimensional neural network when the number of crystal structures for the target protein was limited. We used four different training datasets: one large, general dataset containing various protein complexes and three smaller, more specific datasets containing complexes with CYP3A4-like pockets, complexes with CYP3A4-binding ligands, and complexes with CYP protein family members. We then trained models with different combinations of datasets with or without subsequent fine-tuning and evaluated the binding mode prediction performance of each model. The best receiver operating characteristic (ROC) area under the curve (AUC) model with respect to area under the receiver operating characteristic curve was obtained by training with a combination of the general protein and CYP family datasets. However, the ROC AUC-recall balanced model was obtained by training with this combination of datasets followed by fine-tuning with the CYP3A4-binding ligands dataset. Our results suggest that datasets that balance protein functionality and data size are important for optimizing binding mode prediction performance. In addition, datasets with large median binding pocket sizes may be important for the binding mode prediction specifically of CYP3A4.

Polyvinyl alcohol-iodine induced corneal epithelial injury in vivo and its protection by topical rebamipide treatment.

Periocular povidone-iodine (PI) and polyvinyl alcohol-iodine (PAI) have had a major role in the prevention of endophthalmitis. The purpose of this study was to investigate the corneal epithelial toxicity of PAI in a rabbit eye model using corneal resistance (CR) measurement, which is a good indicator of cell barrier function. Rabbit eyes were administered PAI solution at 4-, 6-, 8-, or 16-fold dilution with physiological saline solution (saline) or saline alone (control), to the conjunctival sac with/without wash-out with saline. Corneal epithelial injury assessed by fluorescein staining and the CR ratio was measured at 10 minutes (min) to 96 hours (h) after the initial administration. Histological observation was performed in the eyes following the PAI or control administrations. At 120 min after administration of PAI solution, the CR ratio was decreased and superficial punctate keratopathy (SPK) was significantly increased in each of the PAI-administered groups compared to the control. Recovery of CR and SPK after administration of 6- or 8-fold dilution of PAI was significantly delayed in eyes that were not subsequently washed with saline compared with eyes that were. Pre- or post-instillation of 2% rebamipide ophthalmic suspension significantly reduced PAI induced-SPK and -decrease of CR ratio. The CR method was able to accurately and quantitatively evaluate fine corneal epithelial injury. It is suggested that eyes should be washed with saline solution after administration of PAI solution or the instillation of rebamipide to prevent or reduce corneal epithelial injury.

Reaction dynamics analysis of a reconstituted Escherichia coli protein translation system by computational modeling.

To elucidate the dynamic features of a biologically relevant large-scale reaction network, we constructed a computational model of minimal protein synthesis consisting of 241 components and 968 reactions that synthesize the Met-Gly-Gly (MGG) peptide based on an Escherichia coli-based reconstituted in vitro protein synthesis system. We performed a simulation using parameters collected primarily from the literature and found that the rate of MGG peptide synthesis becomes nearly constant in minutes, thus achieving a steady state similar to experimental observations. In addition, concentration changes to 70% of the components, including intermediates, reached a plateau in a few minutes. However, the concentration change of each component exhibits several temporal plateaus, or a quasi-stationary state (QSS), before reaching the final plateau. To understand these complex dynamics, we focused on whether the components reached a QSS, mapped the arrangement of components in a QSS in the entire reaction network structure, and investigated time-dependent changes. We found that components in a QSS form clusters that grow over time but not in a linear fashion, and that this process involves the collapse and regrowth of clusters before the formation of a final large single cluster. These observations might commonly occur in other large-scale biological reaction networks. This developed analysis might be useful for understanding large-scale biological reactions by visualizing complex dynamics, thereby extracting the characteristics of the reaction network, including phase transitions.

Molecular signature of quiescent satellite cells in adult skeletal muscle.

Skeletal muscle satellite cells play key roles in postnatal muscle growth and regeneration. To study molecular regulation of satellite cells, we directly prepared satellite cells from 8- to 12-week-old C57BL/6 mice and performed genome-wide gene expression analysis. Compared with activated/cycling satellite cells, 507 genes were highly upregulated in quiescent satellite cells. These included negative regulators of cell cycle and myogenic inhibitors. Gene set enrichment analysis revealed that quiescent satellite cells preferentially express the genes involved in cell-cell adhesion, regulation of cell growth, formation of extracellular matrix, copper and iron homeostasis, and lipid transportation. Furthermore, reverse transcription-polymerase chain reaction on differentially expressed genes confirmed that calcitonin receptor (CTR) was exclusively expressed in dormant satellite cells but not in activated satellite cells. In addition, CTR mRNA is hardly detected in nonmyogenic cells. Therefore, we next examined the expression of CTR in vivo. CTR was specifically expressed on quiescent satellite cells, but the expression was not found on activated/proliferating satellite cells during muscle regeneration. CTR-positive cells reappeared at the rim of regenerating myofibers in later stages of muscle regeneration. Calcitonin stimulation delayed the activation of quiescent satellite cells. Our data provide roles of CTR in quiescent satellite cells and a solid scaffold to further dissect molecular regulation of satellite cells. Disclosure of potential conflicts of interest is found at the end of this article.