Unveiling the role of differential growth in 3D morphogenesis: An inference method to analyze area expansion rate distribution in biological systems.

The three-dimensional (3D) morphologies of many organs in organisms, such as the curved shapes of leaves and flowers, the branching structure of lungs, and the exoskeletal shape of insects, are formed through surface growth. Although differential growth, a mode of surface growth, has been qualitatively identified as 3D morphogenesis, a quantitative understanding of the mechanical contribution of differential growth is lacking. To address this, we developed a quantitative inference method to analyze the distribution of the area expansion rate, which governs the growth of surfaces into 3D morphology. To validate the accuracy of our method, we tested it on a basic 3D morphology that allowed for the theoretical derivation of the area expansion rate distribution, and then assessed the difference between the predicted outcome and the theoretical solution. We also applied this method to complex 3D shapes and evaluated its accuracy through numerical experiments. The findings of the study revealed a linear decrease in error on a log-log scale with an increase in the number of meshes in both evaluations. This affirmed the reliability of the predictions for meshes that are sufficiently refined. Moreover, we employed our methodology to analyze the developmental process of the Japanese rhinoceros beetle Trypoxylus dichotomus, which is characterized by differential growth regulating 3D morphogenesis. The results indicated a notably high rate of area expansion on the left and right edges of the horn primordium, which is consistent with the experimental evidence of a higher rate of cell division in these regions. Hence, these findings confirm the efficacy of the proposed method in analyzing biological systems.

The draft genome sequence of the Japanese rhinoceros beetle Trypoxylus dichotomus septentrionalis towards an understanding of horn formation.

The Japanese rhinoceros beetle Trypoxylus dichotomus is a giant beetle with distinctive exaggerated horns present on the head and prothoracic regions of the male. T. dichotomus has been used as a research model in various fields such as evolutionary developmental biology, ecology, ethology, biomimetics, and drug discovery. In this study, de novo assembly of 615 Mb, representing 80% of the genome estimated by flow cytometry, was obtained using the 10 × Chromium platform. The scaffold N50 length of the genome assembly was 8.02 Mb, with repetitive elements predicted to comprise 49.5% of the assembly. In total, 23,987 protein-coding genes were predicted in the genome. In addition, de novo assembly of the mitochondrial genome yielded a contig of 20,217 bp. We also analyzed the transcriptome by generating 16 RNA-seq libraries from a variety of tissues of both sexes and developmental stages, which allowed us to identify 13 co-expressed gene modules. We focused on the genes related to horn formation and obtained new insights into the evolution of the gene repertoire and sexual dimorphism as exemplified by the sex-specific splicing pattern of the doublesex gene. This genomic information will be an excellent resource for further functional and evolutionary analyses, including the evolutionary origin and genetic regulation of beetle horns and the molecular mechanisms underlying sexual dimorphism.

RNA Interference Method for Gene Function Analysis in the Japanese Rhinoceros Beetle Trypoxylus dichotomus.

In the Japanese rhinoceros beetle Trypoxylus dichotomus, various candidate genes required for a specific phenotype of interest are listed by next-generation sequencing analysis. Their functions were investigated using RNA interference (RNAi) method, the only gene function analysis tool for T. dichotomusdeveloped so far. The summarized procedure for the RNAi method used for T. dichotomusis to synthesize double-stranded RNA (dsRNA), and inject it in larvae or pupae of T. dichotomus. Although some dedicated materials or equipment are generally required to inject dsRNA in insects, the advantage of the protocol described here is that it is possible to inject dsRNA in T. dichotomuswith one syringe.

Recent advances in understanding horn formation in the Japanese rhinoceros beetle Trypoxylus dichotomus using next-generation sequencing technology.

The exaggerated horns of beetles are attractive models for studying the origin of novel traits and morphological evolution. Closely related species often differ profoundly in the size, number, and shape of their horns, and in the body region from which they extend. In addition, beetle horns exhibit exquisite nutrition-dependent phenotypic plasticity, leading to disproportionate growth of the horns in the largest, best-condition individuals and much smaller - even stunted - horn sizes in poor-condition individuals. These exciting phenomena in beetle horns have recently been revealed at the molecular level with the advent of next-generation sequencing. This section reviews the latest research on a horned beetle, the Japanese rhinoceros beetle Trypoxylus dichotomus, whose genome was recently sequenced.

Adaptation of the Hierarchical Factor Segmentation method to noisy activity data.

The Hierarchical Factor Segmentation (HFS) method is a non-parametric statistical method for detection of the phase of a biological rhythm shown in an actogram. The detection accuracy of this method was measured on actograms showing only circadian rhythms with a constant ratio of signal to noise (S/N). In the present study, we generated 84 types of artificial actograms including circadian or circatidal rhythms by using three parameters: α/ρ, S/N and period length τ, and evaluated the effectiveness of our devised adaptation of the HFS method, the cycle-by-cycle adaptation. The results showed the effectiveness of the cycle-by-cycle adaptation was high even though S/N or τ was fluctuating through a whole actogram. These suggested that the cycle-by-cycle adaptation could be effectively applied to various kinds of rhythmic activity data. The C++ source code of the cycle-by-cycle adaptation is available on the website at https://github.com/KazukiSakura/cHFS.git .