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Cyclin-dependent kinase-like 5 (CDKL5) is a serine/threonine protein kinase whose pathological mutations cause CDKL5 deficiency disorder. Most missense mutations are concentrated in the catalytic domain. Therefore, anticipating whether mutations in this region affect CDKL5 function is informative for clinical diagnosis. This study comprehensively predicted the pathogenicity of all 5700 missense substitutions in the catalytic domain of CDKL5 using in silico analysis and evaluating their accuracy. Each missense substitution was evaluated as “pathogenic” or “benign”. In silico tools PolyPhen-2 HumDiv mode/HumVar mode, PROVEAN, and SIFT were selected individually or in combination with one another to determine their performance using 36 previously reported mutations as a reference. Substitutions predicted as pathogenic were over 88.0% accurate using each of the three tools. The best performance score (accuracy, 97.2%; sensitivity, 100%; specificity, 66.7%; and Matthew’s correlation coefficient (MCC), 0.804) was achieved by combining PolyPhen-2 HumDiv, PolyPhen-2 HumVar, and PROVEAN. This provided comprehensive information that could accurately predict the pathogenicity of the disease, which might be used as an aid for clinical diagnosis.

Histone acetylation and deacetylation are associated with diverse biological phenomena via gene transcription, and histone deacetylases (HDACs) regulate protein deacetylation. HDAC8 is associated with childhood neurological disorders that develop in the uterus and may contribute to neurodevelopment. In our previous studies, we found that HDAC8 regulates neuronal differentiation in P19 pluripotent embryonic carcinoma cells (P19EC cells) by regulating embryoid body (EB) formation. However, the mechanism through which HDAC8 is involved in EB formation and neuronal differentiation remains unclear. Here, we show that HDAC8 regulates EB formation and neuronal differentiation by regulating the canonical Hedgehog (Hh) signaling pathway in P19EC cells. We found that HDAC8 is possibly involved in regulating the expression of the Smoothened receptor (Smo), an important receptor in canonical Hh signaling, and treatment with a Smo agonist restored EB formation ability, which was reduced in HDAC8 knockout P19EC cells. Our results demonstrate that HDAC8 functions in EB formation, which is involved in the Hh signaling pathway that is important for embryonic development.

P19 pluripotent embryonic carcinoma (EC) stem cells are derived from pluripotent germ cell tumours and can differentiate into three germ layers. Treatment of these cells in suspension culture with retinoic acid induces their differentiation into neurons and glial cells. Hence, these cells are an excellent in vitro model to study the transition from the upper blastoderm to the neuroectoderm. However, because of the complex nature of the techniques involved, the results are highly dependent on the skills of the experimenter. Herein, we developed a simple method to induce neuronal differentiation of adherent P19 EC cells in TaKaRa NDiff® 227 serum-free medium (originally N2B27 medium). This medium markedly induced neuronal differentiation of P19 EC cells. The addition of retinoic acid to the NDiff® 227 medium further enhanced differentiation. Furthermore, cells differentiated by the conventional method, as well as the new method, showed identical expression of the mature neuronal marker, neuronal nuclei. To determine whether our approach could be applied for neuronal studies, we measured histone deacetylase 8 (HDAC8) activity using an HDAC8 inhibitor and HDAC8-knockout P19 EC cells. Inhibition of HDAC8 activity suppressed neuronal maturation. Additionally, HDAC8-knockout cell lines showed immature differentiation compared to the wild-type cell line. These results indicate that HDAC8 directly regulates the neuronal differentiation of P19 EC cells. Thus, our method involving P19 EC cells can be used as an experimental system to study the nervous system. Moreover, this method is suitable for screening drugs that affect the nervous system and cell differentiation.

Histone acetylation and deacetylation correlate with diverse biological phenomena through gene transcription. Histone deacetylases (HDACs) regulate deacetylation of histones and other proteins. However, as a member of the HDAC family, HDAC8 function during neurodevelopment is currently unknown. Therefore, we investigated HDAC8 function during neurodevelopment by examining embryoid body (EB) formation in P19 cells. HDAC8-selective inhibitor (NCC-149) (HDAC8i)-treated cells showed smaller EBs than non-treated cells, as well as reduced expression levels of the neuronal marker, NeuN. Additionally, HDAC8i treatment led to inhibition of cellular proliferation by G2/M phase accumulation and downregulated cyclin A2 and cyclin B1 gene expression. Furthermore, two independent HDAC8 knockout cell lines were established by CRISPR-Cas9, which resulted in smaller EBs, similar to HDAC8i-treated cells. These results suggest that HDAC8 regulates neural differentiation by exerting control of EB formation.

A new high-speed manipulation model for a group of individual bodies (GIB) such as sand and lava is proposed in this paper. One of the goals of this research is to use it for applications such as home VR cooking systems for representing eg. a mass of fried rice. In this model, GIB is represented as a height field. Variation in the height field represents movement of the GIB. Transformation of GIB in wide spaces which is beyond adjacent grids is considered. GIB is treated as one object, which means that calculation is done efficiently on one object. Transformation of GIB is calculated quickly. Interactivity has a priority over correct movement of GIB in this model.