Biology subjects

Ogata, N.

Publications and source records attributed to Ogata, N..

7 recordsLinked to original sources

bioRxiv2026

A Pubic Hair Is 172 Times More Pubic Than a Scalp Hair

Human hair is a common contaminant in GMP-controlled manufacturing environments, and its identification is important for contamination source investigation and corrective action. Because human hair can originate from multiple body sites, it is often necessary to determine not only the species of origin but also the anatomical source of the hair. Conventional forensic approaches distinguish scalp hair from body hair by microscopic examination of cuticle patterns, medullary structure, cross-sectional morphology, and pigment distribution. However, these methods depend on examiner expertise, are difficult to apply to damaged specimens, and provide limited quantitative information. In this study, we developed a proteomics-based approach for distinguishing scalp hair from pubic hair using identical sample preparation and analytical workflows. Comparative proteomic analysis identified keratin-associated proteins KAP 4-3 and KAP 9-6 as enriched in scalp hair, whereas cuticular keratins Ha7 and Ha8 were strongly enriched in pubic hair. Amino acid composition analysis further revealed that scalp hair-enriched proteins were highly cysteine-rich, consistent with sulfur-rich cross-linking matrix proteins, whereas pubic hair-enriched proteins exhibited characteristics of structural keratin filaments. These results demonstrate that proteomic signatures can provide a quantitative and objective means of determining the anatomical origin of human hair and may contribute to contamination source tracing in GMP manufacturing and forensic investigations.

bioengineering↗

bioRxiv2026

Human-Dog Interaction Method and Dog Familiarity Differentially Modulate Prefrontal Connectivity and Autonomic Recovery Following Acute Stress: An fNIRS Study

Human-dog interaction is widely used to alleviate stress, yet the accompanying cortical and autonomic dynamics during acute stress and recovery remain incompletely characterized. In this study, 70 adult dog owners completed a standardized stress protocol while prefrontal cortex activity was continuously monitored with functional near-infrared spectroscopy (fNIRS), alongside subjective stress and salivary cortisol measures. Participants then underwent a recovery phase involving interaction with a companion dog, manipulating contact type (direct in person vs. indirect video conferencing), and familiarity (own vs. unfamiliar dog). Stress responses were quantified through heart rate (HR), heart rate variability (HRV), low- and high-frequency spectral power (LF, HF, and LF/HF), and prefrontal functional connectivity (FC) based on maximum cross-correlation coefficients between fNIRS channels. As expected, HR, HRV-derived indices, and FC increased from baseline to the stress phase, confirming robust engagement of autonomic and prefrontal networks. During the recovery phase, all dog interaction conditions demonstrated reductions in HR, LF/HF ratio, and FC toward or below baseline, consistent with physiological and neural stress recovery; direct interaction was associated with particularly pronounced parasympathetic enhancement and a drop in FC that fell significantly below baseline in some cases. Across groups, HRV, LF/HF, and FC were the most consistent predictors of subjective stress ratings, whereas associations with cortisol were limited. These findings suggest that human-dog interaction promotes coordinated autonomic and prefrontal recovery from acute stress, and that fNIRS-derived metrics might provide a marker of stress modulation that can distinguish high-cognitive load and low cognitive demand states beyond traditional stress indices.

neuroscience↗

bioRxiv2025

Database Chemistry for Genomics-Based Safety and Quality Evaluation of Biologics

Genomics-based safety and quality evaluation studies are advancing the bioindustry by enhancing various aspects, including viral safety, host cell protein (HCP) control, product heterogeneity control, cellular heterogeneity control, and process reproducibility. High-throughput instruments and genome-scale databases are essential in genomics, with the reference genome sequence being the most critical database. The completeness and accuracy of these genome sequences depend on DNA quality, sequencing instruments, read coverage, and assembly strategies. Significant efforts are being made to perfect genome assembly and continuously improve it. However, the quantitative impact of reference genome sequence accuracy on the safety of biologics is not yet fully understood. In this study, we compared and benchmarked six Chinese hamster genomes, including four newly sequenced genomes derived from Chinese hamster cell lines, from an industrial perspective. We also developed database assembly techniques to enhance the safety of biologics. We recommend using two or more independent reference genomes for viral safety studies. For HCP control, we suggest using protein sequences in which trypsin degradation peptides that overlap with high-risk proteins should be masked and unified. Additionally, we can predict microenvironments using single-cell transcriptome data. In bioengineering processes, any nucleotide samples have potential commercial benefits.

bioengineering↗

bioRxiv2024

Liberality is More Explainable than PCA of Transcriptome for Vertebrate Embryo Development

Dimensional reduction approaches of genome scale data are widely used. Liberality is one of the approaches which is a quantitative index of cellular differentiation and dedifferentiation. Here, we analyzed a trend of liberality of time course transcriptome data on vertebrate embryo development. Historically annotated embryo developmental stages matched changes in the trend of liberality. Analyzing liberality of various biological phenomena would be beneficial.

bioinformatics↗

bioRxiv2024

A positive list administered immunity system restricts the body size of insects

There are several explanations for the extinction of ancient giant insects. Here, we present a new hypothesis suggesting that the innate immune system limits the body sizes of insects. In this study, we co-cultured bacteria, fungi, and insect blood cells, and performed single-cell RNA sequencing analyses of insect blood cells to determine their division of labor. In the innate immune system, prohibited molecules are listed as signals of invasion. The increasing diversity of organisms makes this list extensive. The burden of managing such an extensive list leads to a division of labor among blood cells and reduces the effective number of blood cells. Our simulation indicates that a reduced number of effective blood cells cannot protect a giant body from invaders.

immunology↗

bioRxiv2019

Synergic Interaction between Permethrin and Bt toxins discovered using RNA-seq

Acting against the development of resistance to antibiotics and insecticides, involving negatively correlated cross-resistance (NCR) is an alternative to use- and-discard approach. It is termed NCR that toxic chemicals interact with each other and resistance of target organisms to one chemical is sometimes associated with increased susceptibility to a second chemical when; an allele confers resistance to one toxic chemical and hyper-susceptibility to another, NCR occurs. However, only 11 toxin pairs have been revealed to cause NCR in insects. Finding novel NCRs is needed for integrated pest management. We analyzed permethrin, an insecticide, induced transcriptomes of cultured fat bodies of the silkworm Bombyx mori, a lepidopteran model insect. Differentially expressed gene analyses suggested Bacillus thuringiensis (Bt) toxin was an NCR toxin of permethrin. NCR to permethrin and Bt toxins in Thysanoplusia intermixta, the agricultural pest moth, was examined; the children of permethrin survivor T. intermixta had increased susceptibility to Bt toxin. A novel NCR toxin pair, permethrin and Bt toxin, was discovered. The screening and developmental method for negatively correlated cross-resistance toxins established in this study was effective, in vitro screening using model organisms and in vivo verification using agricultural pests.

zoology↗

bioRxiv2019

Transcriptome Dedifferentiation Observed in Animal Primary Cultures is Essential to Plant Reprogramming

Tissue culture environment liberate cells from ordinary laws of multi-cellular organisms. This liberation enables cells several behaviors, such as growth, dedifferentiation, acquisition of pluripotency, immortalization and reprogramming. Each phenomenon is relating to each other and hardly to determine. Recently, dedifferentiation of animal cell was determined and quantified in increasing information entropy of transcriptome. The increasing information entropy of transcriptome induced by tissue culture may reappear in plant cells too. Here we corroborated it. Measuring information entropies of transcriptomes during reprogramming of plant cells suggested that reprogramming is a combined phenomenon of dedifferentiation and re-differentiation.

plant biology↗