Biology subjects

Ishida, S.

Publications and source records attributed to Ishida, S..

16 recordsLinked to original sources

bioRxiv2026

A rapidly deployable CRISPR-Cas3 diagnostic platform for emerging RNA viruses

Rapidly converting viral genome information into deployable molecular tests remains a major challenge in outbreak preparedness. We developed CONAN-SWIFT (Simple Workflow for Isothermal Field Testing), a sequence-to-test platform that integrates computational assay design, reverse-transcription loop-mediated isothermal amplification, CRISPR-Cas3 detection, reagent lyophilization and lateral-flow readout. Sequence-guided assays for Andes virus and Bundibugyo virus were established within approximately three weeks and extended to four additional filoviruses. A web-based designer supported crRNA selection, and systematic RT-LAMP primer optimization improved amplification performance. Recombinant Escherichia coli-expressed Cascade enabled standardized preparation of lyophilized Cas3-detection reagents, which were combined with a battery-operated isothermal device. The portable system detected as few as 10 input RNA copies per reaction within approximately 40 min. It also detected viral RNA and biologically contained, replication-incompetent Ebola virus in spiked human blood and concentrated wastewater. These findings establish the analytical feasibility of a rapidly adaptable CRISPR-Cas3 engineering framework for decentralized detection of emerging RNA viruses.

bioengineering↗

bioRxiv2025

Assessing the Performance of LLMs in Multimodal Information Extraction for Biological Research: A Case Study on LLPS

Advances in experimental techniques have expanded the volume of biological data. This has increased the demand for structured information extraction from papers, with large language models (LLMs) considered promising. However, challenges remain, including limited validation in biology and unclear applicability to multimodal tasks that integrate text with domain-specific figures, such as microscopic images and scatter plots. Here, we developed a multimodal LLM (MLLM)-based workflow to extract the experimental conditions and phase status from the text and figures of experimental papers on liquid-liquid phase separation and validated the effect of various inputs, prompts, and MLLM types. As a result, the Gemini 2.5 Pro-based extraction achieved an F1-score of 0.847 by processing each figure as a processing unit and inputting domain-specific prompts reflecting manual extraction guidance. This study demonstrates the potential and limitations of MLLMs for extracting biological information and provides insights for advancing multimodal approaches in biology.

bioinformatics↗

bioRxiv2025

Lamin B1 physically regulates neuronal migration by modulating nuclear deformability in the developing cortex

Neuronal migration is a vital process that positions billions of neurons to create a functional brain. To navigate the constrained microenvironments within the cortex, precise control over the nuclear mechanics in migrating neurons is indispensable. Here, we show that Lamin B1 (LB1) regulates neuronal migration by modulating nuclear deformability. Excess LB1 in neurons halted migration without altering laminar identity or overall gene expressions in vivo, while in vitro, it elevated nuclear stiffness and impaired neuronal motility in confined spaces. Moreover, mispositioned neurons resulted in electrophysiological defects in the brain. Computational modeling predicted a temporal relationship between nuclear deformation and enhanced migration velocity, which was validated experimentally through live imaging. Notably, cerebral organoid assays using iPS cells established from patients with LMNB1 duplication exhibited impaired neuronal migration in a human model. Collectively, these findings demonstrate that LB1 is a critical regulator of nuclear mechanics, ensuring the accurate spatiotemporal positioning of neurons.

neuroscience↗

bioRxiv2025

Human pluripotent stem cell-derived intestinal epithelial cells maintain small intestine-specific functions over time, even with repeated cell division

The human colon cancer-derived cell line Caco-2 is widely used in drug discovery due to its barrier function and transporter activity. However, Caco-2 cells have extremely low drug metabolic capacity, resulting in discrepancies with human physiology. In this study, we conducted experiments on human intestinal epithelial cells generated from pluripotent stem cell-derived organoids. We assessed cell morphology, gene expression, barrier and transporter functions, drug metabolic capacity, and cytotoxicity in relation to cell growth and the effects of cellular aging. The results indicate that organoid-derived intestinal epithelial cells may be helpful as a new model cell for drug discovery. Understanding the advantages of drug metabolic capacity and cytotoxicity among cryopreserved human enterocytes, the human colon cancer-derived cell line Caco-2, and human pluripotent stem cell-derived intestinal epithelial cells within microphysiological systems and organ-on-chip technologies is essential for the development of an appropriate model system for the small intestine.

cell biology↗

bioRxiv2025

Directed evolution of a SelB variant that does not require a SECIS element for function

In bacteria the incorporation of selenocysteine is achieved through the interaction of the selenocysteine specific elongation factor (SelB) with selenocysteine-charged tRNASec and a selenocysteine insertion sequence (SECIS) element adjacent to an opal stop codon in a mRNA. The more generalized, SECIS-independent incorporation of selenocysteine is of interest because of the high nucleophilicity of selenium and the greater durability of diselenide bonds. It is likely that during the course of evolution selenocysteine insertion originally arose without the presence of a SECIS element, relying only on SelB. Herein we undertake experiments to evolve an ancestral version of SelB that is SECIS-independent and show that not only can this protein (SelB-v2) generally incorporate selenocysteine across from stop codons, but also that the new, orthogonal translation factor can be repurposed to other amino acids, such as serine. Given the delicate energetic balancing act already performed by EF-Tu, this achievement raises the possibility that greatly expanded genetic codes that relied in part on SelB-based loading can now be contrived.

synthetic biology↗

bioRxiv2023

Human intestinal organoid-derived PDGFRα+ mesenchymal stroma empowers LGR4+ epithelial stem cells

The columnar epithelial cells comprising the intestinal tract, stomach, and uterus can be cultured in vitro as organoids or in adherent culture. However, the proliferation of these columnar epithelial cells in adherent culture is limited. Likewise, human pluripotent stem cell (hPSC)-derived intestinal epithelial cells do not show extensive or clonal propagation in vitro. In this study, we induced proliferation of hPSC-derived small intestinal epithelium for a longer time by utilizing mesenchymal stromal cells derived from self-organized intestinal organoids as feeders. The proliferating cells exhibited columnar form, microvilli and glycocalyx formation, and cell polarity, as well as expression of drug-metabolizing enzymes and transporters. It is noteworthy that small intestinal epithelial stem cells cannot be cultured in adherent culture alone, and the stromal cells cannot be replaced by other feeders. Organoid-derived mesenchymal stromal cells resemble the trophocytes essential for maintaining small intestinal epithelial stem cells, and play a crucial role in adherent culture. The high proliferative expansion, productivity, and functionality of hPSC-derived small intestinal epithelial stem cells could have potential applications in pharmacokinetic and toxicity studies and regenerative medicine.

cell biology↗

bioRxiv2023

Changes in coding and efficiency through modular modifications to a One Pot PURE system for in vitro transcription & translation

The incorporation of unnatural amino acids are attractive methods for improving or bringing new and novel functions in peptides and proteins. Cell-free protein synthesis using the Protein Synthesis Using Recombinant Elements (PURE) system is an attractive platform for efficient unnatural amino acid incorporation. In this work, we further adapted and modified the One Pot PURE for a robust and modular system of enzymatic single site-specific of unnatural amino acid. We demonstrated the flexibility of this system through the introduction of two orthogonal aminoacyl tRNA synthetases and the suppression of two distinctive stop codons.

synthetic biology↗

bioRxiv2023

Predicting condensate formation of protein and RNA under various environmental conditions

MotivationLiquid-liquid phase separation (LLPS) by biomolecules plays a central role in various biological phenomena and has garnered significant attention. The behavior of LLPS is strongly influenced by the characteristics of the RNAs and environmental factors such as pH and temperature, as well as the properties of the proteins. Recently, several databases of biomolecules associated with LLPS have been established, and prediction models of LLPS-related phenomena have been explored, leveraging these databases. However, a prediction model that concurrently considers proteins, RNAs, and experimental conditions has not been developed due to the limited information available from individual experiments in public databases. ResultsTo address this challenge, we have built a new dataset called RNAPSEC, which serves each individual experiment as a data point. This dataset was accomplished by manually collecting data from public literature. Utilizing RNAPSEC, we developed two distinct models that consider a protein, RNA, and experimental conditions. The first model can predict the LLPS behavior of a protein and RNA under specific conditions. The second model can predict the required conditions for a given protein and RNA to undergo LLPS. RNAPSEC and these prediction models are expected to accelerate our understanding of the roles of proteins, RNAs, and environmental factors in LLPS. AvailabilityThe codes for the prediction models and RNAPSEC are available at https://github.com/ycu-iil/RNAPSEC. Contactterayama@yokohama-cu.ac.jp

bioinformatics↗

bioRxiv2023

In depth amino acid mutational analysis of the key interspecific incompatibility transmembrane factor Stigmatic Privacy 1

O_LIIn plants, there is an active prezygotic interspecific-incompatibility mechanism to prevent unfavorable hybrids between two species. We previously reported that an uncharacterized protein with four-transmembrane domains, named as Stigmatic Privacy 1 (SPRI1), is responsible for rejecting hetero-specific pollen grains in Arabidopsis thaliana. C_LIO_LIWe have conducted a functional study of the SPRI1 protein, via point-mutational experiments and biochemical analysis. We studied the molecular regulatory mechanisms of SPRI1 and the relationships with its function. C_LIO_LIThe alanine- and glycine-scanning experiments together with the evolutional analysis showed that the structural integrity of the C-terminal regions of the extracellular domain of this protein is important for its function. In addition, we found two cysteines (C67 and C80) within the extracellular domain that may be involved in the formation of intermolecular disulfide bonds. SPRI1 may form homo-multimers and is present as part of a ca. 300 kDa complex. C_LIO_LIOur present study indicates that molecular complex formation ability of SPRI1 may be important to maintain its stability and interspecific incompatibility functions in cells. C_LI

plant biology↗

bioRxiv2021

Txn1 mutation causes epilepsy associated with vacuolar degeneration in the midbrain

Thioredoxin (TXN), encoded by Txn1, acts as a critical antioxidant in the defense against oxidative stress by regulating the dithiol/disulfide balance of interacting proteins. The role of TXN in the central nervous system (CNS) is largely unknown. A phenotype-driven study of N-ethyl-N-nitrosourea-mutated rats with running seizures at around five-week of age revealed the relevance of Txn1 mutations to CNS disorders. Genetic mapping identified Txn1-F54L in epileptic rats. The insulin-reducing activity of Txn1-F54L rats was approximately one-third that of the wild-type. Vacuolar degeneration in the midbrain, mainly in the thalamus and the inferior colliculus, was observed in the Txn1-F54L rats. The lesions displayed neuronal and oligodendrocyte cell death. Neurons in Txn1-F54L rats showed morphological changes in the mitochondria. Vacuolar degeneration began at three weeks of age, and spontaneous repair began at seven weeks; a dramatic change from cell death to repair occurred in the midbrain during a restricted period. In conclusion, Txn1 is essential for the development of the midbrain in juvenile rats.

neuroscience↗

bioRxiv2020

Switching secretory pathway direction for organelle acquisition in plants

Eukaryotic cells acquired novel organelles during evolution through mechanisms that remain largely obscure. The existence of the unique oil body compartment is a synapomorphy of liverworts that represents lineage-specific acquisition of this organelle during evolution, although its origin, biogenesis, and physiological function are yet unknown. We found that two Syntaxin 1 paralogs in the liverwort, Marchantia polymorpha, are distinctly targeted to forming cell plates and the oil body, suggesting these structures share some developmental similarity. Oil body formation is under the regulation of an ERF/AP2-type transcription factor and loss of the oil body increased M. polymorpha herbivory. These findings highlight a common strategy for the acquisition of organelles with distinct functions in plants, via periodical switching in secretion direction depending on cellular phase transition.

plant biology↗

bioRxiv2020

Extraction of Protein Dynamics Information Hidden in Cryo-EM Map Using Deep Learning

Technical breakthroughs in cryogenic electron microscopy (cryo-EM)-based single-particle analysis have enabled the structures of numerous proteins to be solved at atomic or near-atomic resolutions, including extremely large macromolecules whose structures could not be solved by conventional techniques. Determining the dynamics properties of these macromolecules, based on their solved structures, can further improve our understanding of their functional mechanisms. However, such analysis is often hampered by the large molecular size and complex structural assembly, making both experimental and computational approaches to determine dynamics properties challenging. Here, we report a deep learning-based approach, DEFMap, to extract the dynamics information "hidden" in cryo-EM density maps. By relying only on cryo-EM maps, DEFMap successfully provided dynamics information equivalent to that determined from molecular dynamics (MD) simulations and experimental approaches at the atomic and residue levels. Additionally, DEFMap could detect dynamics changes associated with molecular recognition and the accompanying allosteric conformational stabilizations, which trigger various biological events such as signal transduction and enzyme catalysis. This approach will provide new insights into the functional mechanisms of biological molecules, accelerating modern molecular biology researches. Furthermore, this advanced strategy combining experimental data, deep learning approaches, and MD simulations would open a new multidisciplinary science area

molecular biology↗

bioRxiv2019

Immortalization of human zone I hepatocytes from biliary atresia with CDK4R24C, cyclin D1, and TERT for cytochrome P450 induction testing

BackgroundHepatocytes are an important tool for in vitro toxicology testing. In addition to primary cultures, a limited number of immortalized cell lines have been developed. We here describe a new cell line, designated as HepaMN, which has been established from a liver associated with biliary atresia.\n\nMethodsHepatocytes were isolated from a liver of 4-year-old girl with biliary atresia and immortalized by inoculation with CSII-CMV-TERT, CSII-CMV-Tet-Off, CSII-TRE-Tight-cyclin D1 and CSII-TRE-Tight-CDK4R24C (mutant CDK4: an INK4a-resistant form of CDK4) lentiviruses at the multiplicity of infection of 3 to 10.\n\nResultsHepaMN cells exhibited morphological homogeneity, displaying hepatocyte-like phenotypes. Phenotypic studies in vivo and in vitro revealed that HepaMN cells showed polarized and functional hepatocyte features along with a canalicular cell phenotype under defined conditions, and constitutively expressed albumin and carbamoyl phosphate synthetase I in addition to epithelial markers. Since HepaMN cells are immortal and subcloned, kinetics and expression profiles were independent of population doublings.\n\nConclusionsHepaMN cells showed increased CYP3A4 expression after exposure to rifampicin, implying that their close resemblance to normal human hepatocytes makes them suitable for research applications including drug metabolism studies.

cell biology↗

bioRxiv2019

Lateral organ diversification in plants mediated by the ALOG protein family of transcription factors

Land plant shoot structures evolved a diversity of lateral organs as morphological adaptations to the terrestrial environment, in which lateral organs independently evolved in each lineage in the sporophyte or gametophyte generation. The gametophyte meristem of the basally-diverging plant Marchantia polymorpha produces axes with non-photosynthetic scale-like lateral organs instead of leaves. Here we report that an ALOG (Arabidopsis LSH1 and Oryza G1) family protein in Marchantia, MpTAWAWA1 (MpTAW1), regulates meristem maintenance and lateral organ development. A mutation in MpTAW1, preferentially expressed in lateral organs, induces lateral organs with mis-specified identity and increased cell number, and furthermore, causes defects in apical meristem maintenance. Remarkably, MpTAW1 expression rescued the elongated-spikelet phenotype of a rice mutant of MpTAW1 homologue. This suggests that ALOG genes are co-opted to specify lateral organ identities in both gametophyte and sporophyte shoots by repressing lateral organ growth. We propose that the recruitment of ALOG-mediated lateral organ modification was in part responsible for the convergent evolution of independently-evolved lateral organs among highly divergent plant lineages and contributed to the morphological diversification of land plants.

plant biology↗

bioRxiv2018

Heterotypic inter-GPCR β-arrestin coupling regulates lymphatic endothelial junctional architecture in murine lymph nodes

Lysophosphatidic acid (LPA) and sphingosine 1-phosphate (S1P) activate G protein-coupled receptors (GPCRs) to regulate key pathobiological processes. Here we report a novel lipid mediator GPCR cross-talk mechanism that modulates lymphatic endothelial junctional architecture in lymph nodes. LPAR1 was identified as an inducer of S1PR1/ {beta}-arrestin coupling from a genome-wide CRISPR/ Cas9 transcriptional activation screen. LPAR1 activation induced S1PR1 {beta}-arrestin recruitment while suppressing Gi protein signaling. Lymphatic endothelial cells from cortical and medullary sinuses of lymph nodes which express LPAR1 and S1PR1, exhibit porous junctional architecture and constitutive S1PR1 coupling to {beta}-arrestin which was suppressed by the LPAR1 antagonist AM095. In endothelial cells, LPAR1-activation increased trans-endothelial permeability and junctional remodeling from zipper-like structures to puncta of adhesion plaques that terminate at actin-rich stress fibers with abundant intercellular gaps. Cross-talk between LPA and S1P receptors regulates complex junctional architecture of lymphatic sinus endothelial cells, a site of high lymphocyte traffic and lymph flow.

cell biology↗

bioRxiv2018

Efficient CRISPR/Cas9-based genome editing and its application to conditional genetic analysis in Marchantia polymorpha

Marchantia polymorpha is one of the model species of basal land plants. Although CRISPR/Cas9-based genome editing has already been demonstrated for this plant, the efficiency was too low to apply to functional analysis. In this study, we show the establishment of CRISPR/Cas9 genome editing vectors with high efficiency for both construction and genome editing. Codon optimization of Cas9 to Arabidopsis achieved over 70% genome editing efficiency at two loci tested. Systematic assessment revealed that guide sequences of 17 nt or shorter dramatically decreased this efficiency. We also demonstrated that a combinatorial use of this system and a floxed complementation construct enabled conditional analysis of a nearly essential gene. This study reports that simple, rapid, and efficient genome editing is feasible with the series of developed vectors.

plant biology↗