Biology subjects

Satoh, S.

Publications and source records attributed to Satoh, S..

15 recordsLinked to original sources

bioRxiv2026

Ecological drivers of social complexity: the role of predation risk and nesting resource in group-living cichlid

Understanding how social complexity responds to environmental variation remains a longstanding challenge in evolutionary biology. Here, we investigated the drivers of social complexity using intraspecific social variation across seven locations of the obligatory shell-brooding cichlid Neolamprologus meeli in Lake Tanganyika. We quantified the number of subordinate individuals per female territory and examined the effects of predation risk, shell availability, and their interaction. Social complexity increased with shell availability under high predation risk but showed little association under low predation risk. A field manipulative-experiment further demonstrated that increasing shell availability led to higher juvenile retention, indicating a causal effect of territory quality. In addition, removal of subordinates reduced shell availability, suggesting the feedback between group size and territory maintenance. We also assessed genetic population structure based on nuclear SNPs obtained by MIG-seq and found only weak genetic differentiation among localities, suggesting that the observed social variation is unlikely to simply reflect strong genetic subdivision. Together, these results show that predation risk promotes group living, whereas nesting resource availability constrains its extent. Our study highlights that social complexity emerges from the interaction between macro- and micro-ecological factors, providing a mechanistic understanding of the evolution of social complexity and philopatry.

ecology↗

bioRxiv2026

Description of the embryonic development in the convict cichlid (Amatitlania nigrofasciata)

We provide a detailed description of embryonic development in the convict cichlid (Amatitlania nigrofasciata) from fertilization to hatching at 26 {degrees}C, together with a practical staging table anchored to established teleost reference frameworks. Fertilized eggs were obtained by both natural spawning and artificial fertilization. Unfertilized eggs were ovoid and adhesive, surrounded by a chorion and a sticky mucous layer. Early development proceeded, in broad outline, through the teleost sequence of meroblastic discoidal cleavage, blastula, gastrula, segmentation, and organogenesis. The first cleavage occurred at 1.75 hours post-fertilization (hpf), with subsequent cleavages at 30 min intervals, reaching the 64-cell stage at 4.25 hpf. Cleavage up to the 64-cell stage progressed on a timescale broadly comparable to that reported for other cichlids, whereas the interval from the 64-cell stage to early epiboly was relatively short in this species. The high, sphere, and dome stages occurred at 8, 9, and 10 hpf, respectively, with epiboly initiating at the dome stage. At the dome stage, a marginal thickening interpreted as the presumptive embryonic shield became apparent. During early epiboly, the blastoderm showed pronounced spatial heterogeneity: it was consistently thicker and advanced more rapidly on the prospective embryonic axis side, yielding a readily detectable asymmetry. A morphologically distinct embryonic axis became visible at 40-50% epiboly, and epiboly was completed at 28.5 hpf. Notably, somitogenesis began before epiboly completion (first somites at 85-90% epiboly), indicating temporal overlap between late gastrulation and early segmentation. Major organ primordia became apparent during the overlapping segmentation/organogenesis interval, and hatching occurred around 70 hpf. Newly hatched larvae possessed three pairs of adhesive glands. This staging reference enables reproducible developmental sampling and should facilitate future comparative, mechanistic, and experimental work using the convict cichlid.

developmental biology↗

bioRxiv2025

Development of a vehicle for non-invasive oral administration to facilitate behavioral experiments in fish

Pharmacological approaches are increasingly used in diverse fields of fish biology. However, injection-based administration can induce stress or injury, potentially interfering with the natural physiological and behavioral states of the fish. Here, we present a non-invasive vehicle for oral administration of peptide-based compounds. To demonstrate its utility, the oxytocin receptor antagonist atosiban was administered orally using this vehicle. Atosiban was then qualitatively detected in serum by high-performance liquid chromatography. This study provides a proof of concept for an easy-to-use and minimally disruptive tool for various fish experiments.

animal behavior and cognition↗

bioRxiv2025

The rice ethylene receptor OsERS1 negatively regulates the shoot growth and salt tolerance in rice seedlings

Ethylene is a gaseous plant hormone that regulates various aspects of growth and development. It promotes shoot growth in etiolated rice seedlings, which is crucial for seedling establishment and has significant agricultural implications. Of the five ethylene receptors in rice, OsERS1 is the most abundantly expressed in seedlings. Therefore, we investigated the localization and role of OsERS1 in shoot growth. When expressed in rice protoplasts, OsERS1 was localized in the endoplasmic reticulum. Knockout mutants of OsERS1 exhibited enhanced shoot growth in etiolated seedlings under normal and ethylene-treated conditions. Additionally, the induction of ethylene-responsive genes was increased in the mutants, indicating an elevated ethylene response due to OsERS1 knockout. The mutants also showed increased salt tolerance. In conclusion, our findings suggest that OsERS1 negatively regulates shoot growth and salt tolerance in etiolated rice seedlings.

plant biology↗

bioRxiv2024

Facial Coloration as a Social Signal in a Neotropical Cichlid: Testing the Facial Expression Hypothesis

The face is a uniquely distinctive stimulus, encapsulating a wealth of information. Among the myriad of social cues conveyed by the face, emotional signals, known as facial expressions, are paramount not only for humans but also for numerous social animals. The evolution of facial expressions in these animals can also manifest in taxa other than mammals, as suggested by various studies highlighting the socio-ecological benefits of facial expressions. In this study, we elucidated the social function of facial coloration, determined by melanophores, in the neotropical social cichlid Symphysodon aequifasciatus. In this species, facial coloration exhibits instantaneous changes in response to varying social contexts. Through behavioral observations and experimental manipulation, we confirmed that facial coloration in S. aequifasciatus serves to attenuate unnecessary aggressive competition among conspecifics. Furthermore, we observed that the facial area subjected to coloration in this species is innervated by the adenosine triphosphate- and noradrenaline-ergic nervous system. These findings indicated that facial expression in S. aequifasciatus depends on the sympathetic nervous system and has evolved independently of mammalian facial expressions. Our study highlights teleost fishes as valuable animal models for exploring the universality of facial expressions and their underlying cognitive mechanisms in vertebrates.

animal behavior and cognition↗

bioRxiv2024

Transcription of damage-induced RNA in Arabidopsis was frequently initiated from DSB loci within the genic regions

DNA double-strand breaks (DSBs) are the most severe DNA lesions and need to be removed immediately to prevent loss of genomic information. Recently, it has been revealed that DSBs induce de novo transcription from the cleavage sites in various species, resulting in RNAs being referred to as damage-induced RNAs (diRNAs). While diRNA synthesis is an early event in the DNA damage response and plays an essential role in DSB repair activation, the location where diRNAs are newly generated in plant remains unclear, as does their transcriptional mechanism. Here, we performed RNA sequencing of diRNAs that emerged around all DSB loci in Arabidopsis thaliana under the expression of the exogenous restriction enzyme Sbf I and observed 88 diRNAs in 360 DSB loci. Most of the detected diRNAs originated within the active genes and were transcribed from DSBs in a bidirectional manner. Furthermore, we found that diRNA elongation tends to terminate at the boundary of an endogenous gene located near DSB loci. Our results provide reliable evidence for understanding the importance of de novo transcription at DSBs and show that diRNA is a crucial factor for successful DSB repair.

molecular biology↗

bioRxiv2023

Sperm competition influences sperm quality and seminal plasma protein expression among territorial males of the courtship cichlid

Sperm competition drives the plasticity of sperm quality and seminal fluid. However, how environmental and behavioral factors influence sperm competition and its outcome on the plasticity of sperm quality are unknown. In this study, we show males can asses the sperm competition level, and their fertilization-promoting sperm traits changes according to intensity. The promiscuous Tanganyikan cichlids Ophthalmotilapia ventralis perform their fertilization in the female mouth cavity. Sperm competition occurs in the female mouth as sperm is collected from multiple males. Behavioral (i.e., courtship success rates [CSR]) and environmental (density of spawning sites [DS]) factors are related to sperm collection. Seminal plasma glycoprotein 120 (SPP120) aids in sperm immobilization and aggregation, and sperm quality (longevity and velocity) could increase the probability of siring offspring. Based on an assumption of the involvement of DS and CSR on sperm collection, DS and CSR could influence the expression of SPP120 and sperm quality. We examined how sperm quality and SPP120 affect sperm competition-associated CSR and DS. Sperm longevity and velocity were positively correlated with DS. SPP120 expression was also positively correlated with CSR and DS. The plasticity of sperm quality and amount of SPP120 result in high fertilization competency according to sperm competition level.

evolutionary biology↗

bioRxiv2023

Inducible expression of the restriction enzyme uncovered genome-wide distribution and dynamic behavior of histones H4K16ac and H2A.Z at DNA double-strand breaks in Arabidopsis

DNA double-strand breaks (DSBs) are among the most serious types of DNA damage and cause mutations and chromosomal rearrangements. In eukaryotes, DSBs are immediately repaired in coordination with chromatin remodeling for the deposition of DSB-related histone modifications and variants. To elucidate the details of DSB-dependent chromatin remodeling throughout the genome, artificial DSBs need to be reproducibly induced at various genomic loci. Recently, in mammals, a comprehensive method for elucidating chromatin remodeling at multiple DSB loci via chemically induced expression of a restriction enzyme was developed. However, this DSB induction system is not suitable for investigating chromatin remodeling during and after DSB repair, and such approach has not been performed in plants. Here, we established a transgenic Arabidopsis plant harboring a restriction enzyme gene Sbf I driven by a heat-inducible promoter. Using this transgenic plant, we performed chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) of histones H4K16ac and H2A.Z and investigated dynamics of these histone marks around the endogenous 623 Sbf I recognition sites. We also precisely quantified DSB efficiency at all cleavage sites using the DNA resequencing data obtained by ChIP-seq procedures. From the results, Sbf I-induced DSBs were detected at 360 loci and induced the transient deposition of H4K16ac and H2A.Z around these regions. Interestingly, we also observed the co-localization of H4K16ac and H2A.Z at some DSB loci. Overall, DSB-dependent chromatin remodeling was found to be a highly conserved between plants and animals. These findings provide new insights into chromatin remodeling that occurs in response to DSBs in Arabidopsis.

molecular biology↗

bioRxiv2022

Phylogeny analysis of whole protein-coding genes in metagenomic data detected an environmental gradient for the microbiota

Environmental factors affect the growth of microorganisms and therefore alter the composition of microbiota. Correlative analysis of the relationship between metagenomic composition and the environmental gradient can help elucidate key environmental factors and establishment principles for microbial communities. However, a reasonable method to quantitatively compare whole metagenomic data and identify the primary environmental factors for the establishment of microbiota has not been reported so far. In this study, we developed a method to compare whole proteomes deduced from metagenomic shotgun sequencing data, and quantitatively display their phylogenetic relationships as metagenomic trees. We called this method Metagenomic Phylogeny by Average Sequence Similarity (MPASS). We also compared one of the metagenomic trees with dendrograms of environmental factors using a comparison tool for phylogenetic trees. The MPASS method correctly constructed metagenomic trees of simulated metagenomes and soil and water samples. The topology of the metagenomic tree of samples from the Kirishima hot springs area in Japan was highly similarity to that of the dendrograms based on previously reported environmental factors for this area. The topology of the metagenomic tree also reflected the dynamics of microbiota at the taxonomic and functional levels. Our results strongly suggest that MPASS can successfully classify metagenomic shotgun sequencing data based on the similarity of whole protein-coding sequences, and will be useful for the identification of principal environmental factors for the establishment of microbial communities.

microbiology↗

bioRxiv2020

Cryptic promoter activation occurs by at least two different mechanisms in the Arabidopsis genome

In gene-trap screening of plant genomes, promoterless reporter constructs are often expressed without trapping of annotated gene promoters. The molecular basis of this phenomenon, which has been interpreted as the trapping of cryptic promoters, is poorly understood. In this study, using Arabidopsis gene-trap lines in which a firefly luciferase (LUC) open reading frame (ORF) was expressed from intergenic regions, we found that cryptic promoter activation occurs by at least two different mechanisms: one is the capturing of pre-existing promoter-like chromatin marked by H3K4me3 and H2A.Z, and the other is the entirely new formation of promoter chromatin near the 5 end of the inserted LUC ORF. To discriminate between these, we denoted the former mechanism as "cryptic promoter capturing", and the latter one as "promoter de novo origination". The latter finding raises a question as to how inserted LUC ORF sequence is involved in this phenomenon. To examine this, we performed a model experiment with chimeric LUC genes in transgenic plants. Using Arabidopsis psaH1 promoter-LUC constructs, we found that the functional core promoter region, where transcription start sites (TSS) occur, cannot simply be determined by the upstream nor core promoter sequences; rather, its positioning proximal to the inserted LUC ORF sequence was more critical. This result suggests that the insertion of the LUC ORF sequence alters the local distribution of the TSS in the plant genome. The possible impact of the two types of cryptic promoter activation mechanisms on plant genome evolution and endosymbiotic gene transfer is discussed.

evolutionary biology↗

bioRxiv2020

Plant genome response to incoming coding sequences: stochastic transcriptional activation independent of chromatin configuration

Horizontal gene transfer can occur between phylogenetically distant organisms, such as prokaryotes and eukaryotes. In these cases, how do the translocated genes acquire transcriptional competency in the alien eukaryotic genome? According to the conventional view, specific loci of the eukaryotic genome are thought to provide transcriptional competency to the incoming coding sequences. To examine this possibility, we randomly introduced the promoterless luciferase (LUC)-coding sequences into the genome of Arabidopsis thaliana cultured cells and performed a genome-wide "transgene location vs. expression" scan. We mapped 4,504 promoterless LUC inserts on the A. thaliana chromosomes, and found that about 30% of them were transcribed. Only a small portion of them were explained by the conventional transcriptional fusions with the annotated genes, and the remainder occurred in a quite different manner; (1) they occurred all over the chromosomal regions, (2) independently of the insertion sites relative to the annotated gene loci, inherent transcribed regions, or heterochromatic regions, and (3) with one magnitude lower transcriptional level than the conventional transcriptional fusions. This type of transcriptional activation occurred at about 30% of the inserts, raising a question as to what this 30% means. We tested two hypotheses: the activation occurred at 30% of the entire chromosomal regions, or stochastically at 30% of each insertion event. Our experimental analysis indicates that the latter model could explain this transcriptional activation, a new type of plant genome response to the incoming coding sequences. We discuss the possible mechanisms and evolutionary roles of this phenomenon in the plant genome.

evolutionary biology↗

bioRxiv2020

Kozak sequence acts as a negative regulator for de novo transcription initiation of newborn coding sequences in the plant genome

The manner in which newborn coding sequences and their transcriptional competency emerge during the process of gene evolution remains unclear. Here, we experimentally simulated eukaryotic gene origination processes by mimicking horizontal gene transfer events in the plant genome. We mapped the precise position of the transcription start sites (TSSs) of hundreds of newly introduced promoterless firefly luciferase (LUC) coding sequences in the genome of Arabidopsis thaliana cultured cells. The systematic characterization of the LUC-TSSs revealed that 80% of them occurred under the influence of endogenous promoters, while the remainder underwent de novo activation in the intergenic regions, starting from pyrimidine-purine dinucleotides. These de novo TSSs obeyed unexpected rules; they predominantly occurred ~100 bp upstream of the LUC inserts and did not overlap with Kozak-containing putative open reading frames (ORFs). These features were the output of the immediate responses to the sequence insertions, rather than a bias in the screening of the LUC gene function. Regarding the wild-type genic TSSs, they appeared to have evolved to lack any ORFs in their vicinities. Therefore, the repulsion by the de novo TSSs of Kozak-containing ORFs described above might be the first selection gate for the occurrence and evolution of TSSs in the plant genome. Based on these results, we characterized the de novo type of TSS identified in the plant genome and discuss its significance in genome evolution.

evolutionary biology↗

bioRxiv2020

De novo activated transcription of newborn coding sequences is inheritable in the plant genome

The manner in which inserted foreign coding sequences become transcriptionally activated and fixed in the plant genome is poorly understood. To examine such processes of gene evolution, we performed an artificial evolutionary experiment in Arabidopsis thaliana. As a model of gene-birth events, we introduced a promoterless coding sequence of the firefly luciferase (LUC) gene and established 386 T2-generation transgenic lines. Among them, we determined the individual LUC insertion loci in 76 lines and found that one-third of them were transcribed de novo even in the intergenic or inherently unexpressed regions. In the transcribed lines, transcription-related chromatin marks were detected across the newly activated transcribed regions. These results agreed with our previous findings in A. thaliana cultured cells under a similar experimental scheme. A comparison of the results of the T2-plant and cultured cell experiments revealed that the de novo-activated transcription concomitant with local chromatin remodelling was inheritable. During one-generation inheritance, it seems likely that the transcription activities of the LUC inserts trapped by the endogenous genes/transcripts became stronger, while those of de novo transcription in the intergenic/untranscribed regions became weaker. These findings may offer a clue for the elucidation of the mechanism by which inserted foreign coding sequences become transcriptionally activated and fixed in the plant genome.

evolutionary biology↗

bioRxiv2019

Large DNA virus promoted the endosymbiotic evolution to make a photosynthetic eukaryote

Chloroplasts in photosynthetic eukaryotes originated from a cyanobacterial endosymbiosis far more than 1 billion years ago1-3. Due to this ancientness, it remains unclear how this evolutionary process proceeded. To unveil this mystery, we analysed the whole genome sequence of a photosynthetic rhizarian amoeba4, Paulinella micropora5,6, which has a chloroplast-like organelle that originated from another cyanobacterial endosymbiosis7-10 about 0.1 billion years ago11. Here we show that the predacious amoeba that engulfed cyanobacteria evolved into a photosynthetic organism very quickly in the evolutionary time scale, probably aided by the drastic genome reorganization activated by large DNA virus. In the endosymbiotic evolution of eukaryotic cells, gene transfer from the endosymbiont genome to the host nucleus is essential for the evolving host cell to control the endosymbiont-derived organelle12. In P. micropora, we found that the gene transfer from the free-living and endosymbiotic bacteria to the amoeba nucleus was rapidly activated but both simultaneously ceased within the initiation period of the endosymbiotic evolution, suggesting that the genome reorganization drastically proceeded and completed. During this period, large DNA virus appeared to have infected the amoeba, followed by the rapid amplification and diversification of virus-related genes. These findings led us to re-examine the conventional endosymbiotic evolutionary scenario that exclusively deals with the host and the symbiont, and to extend it by incorporating a third critical player, large DNA virus, which activates the drastic gene transfer and genome reorganization between them. This Paulinella version of the evolutionary hypothesis deserves further testing of its generality in evolutionary systems and could shed light on the unknown roles of large DNA viruses13 in the evolution of terrestrial life.

evolutionary biology↗

bioRxiv2018

High-level expression of STING restricts susceptibility to HBV by mediating type III IFN induction

Hepatitis B virus (HBV) is a hepatotropic DNA virus causing hepatic diseases such as chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. To study HBV, human hepatoma HepG2 cells are currently used as an HBV infectious cell culture model worldwide. HepG2 cells exhibit susceptibility to HBV by exogenously expressing sodium taurocholate cotransporting polypeptide (NTCP). We herein demonstrated that human immortalized hepatocyte NKNT-3 cells exhibited susceptibility to HBV by exogenously expressing NTCP (NKNT-3/NTCP cells). By comparing the cGAS-STING signaling pathway in several NKNT-3/NTCP cell-derived cell clones, we found that STING was highly expressed in cell clones exhibiting resistance but not susceptibility to HBV. High-level expression of STING was implicated in HBV-triggered induction of type III IFN and a pro-inflammatory cytokine, IL-6. In contrast, RNAi-mediated knockdown of STING inhibited type III IFN induction and restored the levels of HBV total transcript in an HBV-infected cell clone exhibiting resistance to HBV. These results suggest that STING regulates susceptibility to HBV by its expression levels.\n\nSTING may thus be a novel target for anti-HBV strategies.

microbiology↗