Japan Research Institute

Alpheus lobidens De Haan, 1849 (type locality: Japan) and A. crassimanus Heller, 1862 (type locality: Nicobar Islands, Andaman Sea), two taxonomically challenging snapping shrimps previously regarded as conspecific, are rediagnosed based on the holotype and on the newly collected material from the Andaman Sea, respectively. Most importantly, the female holotype of A. lobidens has a balaeniceps ridge on the pollex of the minor chela, whereas in A. crassimanus, the minor cheliped fingers of females are simple, devoid of balaeniceps setae. Other characters diagnostic to A. lobidens include the laterally compressed rostrum reaching the distal margin of the first article of the antennular peduncle, the highly elevated rostral carina widening posteriorly, and the broad, deeply depressed adrostral furrows. These features set A. lobidens apart from other taxa previously referred to A. lobidens or A. lobidens complex in literature. Alpheus polynesicus Banner & Banner, 1975, originally described as a subspecies of A. lobidens and later synonymised with A. lobidens, is reinstated as a full species based on evidence from literature. Four new species, which have been confused with A. lobidens, are described from Japan, based on molecular and morphological data, as well as their colour patterns in life: A. yoshigoui sp. nov., A. nigrofasciatus sp. nov., A. latifasciatus sp. nov., and A. aestuaricola sp. nov. These new species are now referred to the A. crassimanus species complex and compared with allied species, including those from outside the Indo-West Pacific. The Japanese records of A. heeia Banner & Banner, 1975 are all referred to A. nigrofasciatus sp. nov. Molecular phylogenetic analyses using two mitochondrial markers (16S rRNA and COI genes) have shown that two morphologically distinct morphs distinguished by the presence or absence of sclerotised setae on the mesial face of the third maxilliped carpus (= penultimate article) belong to the same species, A. nigrofasciatus sp. nov. The taxonomic identities of several lineages of Alpheus recovered in the phylogenetic analyses remain unresolved due to difficulties in accessing voucher specimens. References to A. lobidens and A. crassimanus have been reviewed as thoroughly as possible.

Designing synthetic biomolecular condensates, or membraneless organelles, offers insights into the functions of their natural counterparts and is equally valuable for cellular and metabolic engineering. Choosing E. coli for its biotechnological relevance, we deploy RNA nanotechnology to design and express non-natural membraneless organelles in vivo. The designer condensates assemble co-transcriptionally from branched RNA motifs interacting via base-pairing. Exploiting binding selectivity, we express orthogonal, non-mixing condensates, and by embedding a protein-binding aptamer, we achieve selective protein recruitment. Condensates can be made to dissolve and reassemble upon thermal cycling, thereby reversibly releasing and re-capturing protein clients. The synthetic organelles are expressed robustly across the cell population and remain stable despite enzymatic RNA processing. Compared with existing solutions based on peptide building blocks or repetitive RNA sequences, these nanostructured RNA motifs enable algorithmic control over interactions, affinity for clients, and condensate microstructure, opening further directions in synthetic biology and biotechnology.

ABSTRACTAdult organs exhibit remarkable plasticity, dynamically adjusting their size and function to meet physiological demands. The small‐intestinal epithelium, one of the most rapidly renewing tissues in mammals, undergoes extensive growth and remodeling in response to diet, injury, microbiota changes, and reproduction. Reproduction is an energetically demanding process that requires precise regulation of maternal physiology to support fetal development and neonatal growth. In many mammals including humans, pregnancy induces systemic changes in hormones, metabolism, and immunity. At the organ level, pregnant and lactating females show increases in intestinal size across species such as mice, rats, sheep, and pigs—a phenomenon first documented nearly a century ago. However, the molecular mechanisms governing maternal intestinal remodeling during reproduction, and its physiological significance, remained unclear until recently. Emerging studies, including our recent work, have begun to reveal the cellular changes, molecular mechanisms, and triggers underlying this adaptive growth. This review summarizes current knowledge of intestinal epithelial plasticity in the context of reproduction, integrating findings from both reproductive and non‐reproductive settings. Understanding how the adult intestine adapts to physiological challenges offers valuable insights into developmental biology and has important implications for maternal metabolic health.

We aimed to specify the characteristics of group A Streptococcus M1 (n = 23) or non-M1 (n = 282) isolates from adult (n = 176) and pediatric (n = 129) populations in central Japan, October 2024-April 2025. Of the speA-possessing fourteen non-M1 isolates, there were seven emm3.93 isolates from six non-invasive samples of pediatric patients and one invasive specimen of an adult patient. We found the distribution of M1 clones containing M1_global (n = 1)/M1_13snps (n = 4)/M1_UK (n = 18)-lineages in central Japan of Tokyo/Chiba/Tochigi/Saitama/Kanagawa. The M1 clones were from twenty-one non-invasive samples of pediatric/adult patients and two invasive specimens of adult patients. Additionally, we determined the sic nucleotide alleles and observed the M1_global/M1_13snps/M1_UK sic clustering. Of the CovS amino acid (AA) mutations among M1, there was an insertion of transposase (ISAs1-like IS1548 transposase, 377 AA) into CovS histidine kinase-like ATPase domain (following AA position 458) of one invasive M1_UK isolate. Our observations suggest that CovS AA mutations of invasive isolates with M1_UK should be specified within its four functional domains to evaluate their hypervirulent properties.

Manganese nodules in the Clarion-Clipperton Fracture Zone (CCZ) of the eastern Pacific Ocean have been considered a target for the development of useful metal resources for more than half a century, due to the depletion of onshore resources and advances in mining technology, and are currently the closest to development. Because sediment surface disturbances and suspended plumes are expected to occur due to manganese nodule mining, characterizing sediments in exploitable areas as an environmental baseline is important to minimizing impacts on the marine environment. Here, we report on sediment properties in the Japanese exploration areas, DORD West Area and APEI-10, an area of particular environmental interest, in the western CCZ, where data are scarce compared with the eastern CCZ. We analyzed grain-size composition, chemical composition, and metals, including mercury, to a depth of 20 cm in the sediment. Based on the distribution patterns, metals were divided into group 1 (Mn, Ni, Cu, Zn, Cd, and rare earth elements), group 2 (Fe, Cr, As, and Pb), and group 3 (Hg), with each group observed to be affiliated with manganese oxides, silicate minerals, and organic materials, respectively. Mercury concentrations (<10 ng g−1 to 102 ng g−1) were comparable to those of deep basins; nevertheless, their fluxes were very low, reflecting the limited sedimentation of organic matter. The bulk compositions of the sediments from the western CCZ in this study were similar to those in the eastern-to-central CCZ, although the strong manganese concentrations in the topmost 10 cm of the eastern CCZ were not observed here. We suggest that during the last glacial period, when bottom-water dissolved oxygen concentrations were lower, the east–west gradient of surface primary production and organic matter flux was stronger than today, resulting in less extensive manganese reduction in surface sediments in the western CCZ.

Rare earth elements (REEs) are essential for a clean energy future, high tech, and medicine. For these applications the chemically similar elements need to be tediously separated. Recent discoveries that specific lanthanide-binding proteins such as lanmodulin (LanM) exist in nature have prompted the development of bio-inspired separation methods for REEs. Peptides hold great potential for tuning binding sites in various applications as they are easily synthesised, modifiable, and can be immobilised. Here we use the EF-hand binding site sequences of LanM, the naturally lanthanide-binding EF-hand protein from Methylorubrum extorquens AM1, as a blueprint for peptides with potential applications in REE recycling. We show with time-resolved laser-induced fluorescence spectroscopy (TRLFS), isothermal titration calorimetry (ITC), and nuclear magnetic resonance (NMR) spectroscopy in combination with molecular dynamics (MD) simulations and circular dichroism (CD) spectroscopy the surprising result that reversing the natural sequence of LanM's metal-binding loops leads to an increased binding affinity of about one order of magnitude for three out of four natural sequences. Furthermore, we were able to identify structural features responsible for the affinity boost and were able to obtain - only by exchanging one amino acid - a linear uncapped 12-amino-acid peptide with a 150nM affinity for lanthanides.

This paper reveals that we can interpret the fundamental function of Randomized Time Warping (RTW) as a type of self-attention mechanism, a core technology of Transformers in motion recognition. The self-attention is a mechanism that enables models to identify and weigh the importance of different parts of an input sequential pattern. On the other hand, RTW is a general extension of Dynamic Time Warping (DTW), a technique commonly used for matching and comparing sequential patterns. In essence, RTW searches for optimal contribution weights for each element of the input sequential patterns to produce discriminative features. Although the two approaches look different, these contribution weights can be interpreted as self-attention weights. In fact, the two weight patterns look similar, producing a high average correlation of 0.80 across the ten smallest canonical angles. However, they work in different ways: RTW attention operates on an entire input sequential pattern, while self-attention focuses on only a local view which is a subset of the input sequential pattern because of the computational costs of the self-attention matrix. This targeting difference leads to an advantage of RTW against Transformer, as demonstrated by the 5% performance improvement on the Something-Something V2 dataset.