Biology subjects

Tamada, Y.

Publications and source records attributed to Tamada, Y..

5 recordsLinked to original sources

bioRxiv2026

Comparative study of chlorophyll measurement in Physcomitrium patens moss using a conventional microscope adapted for combined 2D+1D imaging and spectral analysis

Imaging spectroscopy often requires expensive and complex equipment. Here we show a simple procedure for attaching a standard miniature fiber spectrometer to a conventional microscope, allowing easy integration of 2D imaging with 1D high-resolution spectral measurements. This combination provides much of the benefit of a full imaging spectrometer without the large equipment investment, and we provide instructions for modifying microscopes to this setup and the present measurements of living cells that demonstrate their performance. Using this setup, we compare the quantitative measurement of chlorophyll concentration in Physcomitrium patens moss using color imaging and spectral sampling.

bioengineering↗

bioRxiv2026

Abundance versus presence-absence in extinction debt: Time-lagged effects of land use change on salamander populations

Habitat loss and fragmentation have caused global biodiversity loss. It is important to understand the impact of past land use on biodiversity, not only in the present, but also to inform appropriate land-use strategies. Most studies on extinction debt, the concept that past land use drives present organism distribution, focus on species richness. However, when focusing on individual species, species richness is based on presence-absence data and does not reflect abundance. Therefore, extinction debt may not be clearly evident in presence-absence data. However, few studies have compared the effects of past land use on organism distribution using both abundance and presence-absence data. In this study, we compared the effects of past land use on the abundance and presence-absence of the ezo salamander Hynobius retardatus. We surveyed the aquatic areas of Ezo salamander egg sacs along a survey route in northern Japan. We measured the percentages of past and present forest areas, the physical environment, water quality, and waterbody type. The number of egg sacs was significantly associated with the percentage of past forest area, physical environment, water quality, and waterbody type. The presence or absence of egg sacs was significantly associated with the physical environment and water quality. Our results suggest that the effects of past land use on organism distribution are more evident in abundance data than in presence-absence data. Researchers and land managers may need to consider the time lag before extinction based on abundance data to assess extinction risk accurately.

ecology↗

bioRxiv2022

Inhibition of the BMP pathway suppresses tumor growth via downregulation of EGFR in MEK/ERK-dependent colorectal cancer

The bone morphogenetic protein (BMP) pathway promotes differentiation and induces apoptosis in normal colorectal epithelial cells. However, the effect of the BMP pathway in colorectal cancer (CRC) is controversial; it can either be tumor promoting or tumor suppressing, depending on the study. In this study, we found that CRC cells reside in a BMP-rich environment based on RNA-sequencing database analysis. Suppression of BMP using a specific BMP inhibitor, LDN193189, suppresses the growth of organoids in some CRC cases. CRC organoids treated with LDN193189 exhibited a decrease in epidermal growth factor receptor, which was, at least in part, mediated by protein degradation induced by leucine-rich repeats and immunoglobulin-like domains protein 1 (LRIG1). Among CRC organoid panels from 18 different patients, suppression of organoid growth by BMP inhibition correlated with the induction of LRIG1 gene expression. Notably, knockdown of LRIG1 in organoids diminished the growth-suppressive effect of LDN193189. Furthermore, simultaneous treatment with LDN192189 and trametinib, an FDA-approved MEK inhibitor, resulted in a combination effect in both in vivo and in vitro xenograft tumor treatment in CRC organoids, which are susceptible to growth suppression by LDN193189. Taken together, the simultaneous inhibition of BMP and MEK can be a novel treatment option in CRC cases, and evaluating in vitro growth suppression and LRIG1 induction by BMP inhibition using patient-derived organoids could offer functional biomarkers for predicting potential responders.

cancer biology↗

bioRxiv2021

Novel cancer subtyping method based on patient-specific gene regulatory network

The identification of cancer subtypes is important for the understanding of tumor heterogeneity. In recent years, numerous computational methods have been proposed for this problem based on the multi-omics data of patients. It is widely accepted that different cancer subtypes are induced by different molecular regulatory networks. However, only a few incorporate the differences between their molecular systems into the classification processes. In this study, we present a novel method to classify cancer subtypes based on patient-specific molecular systems. Our method quantifies patient-specific gene networks, which are estimated from their transcriptome data. By clustering their quantified networks, our method allows for cancer subtyping, taking into consideration the differences in the molecular systems of patients. Comprehensive analyses of The Cancer Genome Atlas (TCGA) datasets applied to our method confirmed that they were able to identify more clinically meaningful cancer subtypes than the existing subtypes and found that the identified subtypes comprised different molecular features. Our findings show that the proposed method, based on a simple classification using the patient-specific molecular systems, can identify cancer subtypes even with single omics data, which cannot otherwise be captured by existing methods using multi-omics data.

bioinformatics↗

bioRxiv2018

Single-cell transcriptome analysis of Physcomitrella leaf cells during reprogramming using microcapillary manipulation

BackgroundNext-generation sequencing technologies have made it possible to carry out transcriptome analysis at the single-cell level. Single-cell RNA-sequencing (scRNA-seq) data provide insights into cellular dynamics, including intercellular heterogeneity as well as inter- and intra-cellular fluctuations in gene expression that cannot be studied using populations of cells. The utilization of scRNA-seq is, however, restricted to specific types of cells that can be isolated from their original tissues, and it can be difficult to obtain precise positional information for these cells in situ.\n\nResultsHere, we established single cell-digital gene expression (1cell-DGE), a method of scRNA-seq that uses micromanipulation to extract the contents of individual living cells in intact tissue while recording their positional information. Furthermore, we employed a unique molecular identifier to reduce amplification bias in the cDNA libraries. With 1cell-DGE, we could detect differentially expressed genes (DEGs) during the reprogramming of leaf cells into stem cells in excised tissues of the moss Physcomitrella patens, identifying 6,382 DEGs between cells at 0 h and 24 h after excision. We found substantial variations in both the transcript levels of previously reported reprogramming factors and the overall expression profiles between cells, which appeared to be related to their different reprogramming abilities or the estimated states of the cells according to the pseudotime based on the transcript profiles.\n\nConclusionsWe developed 1cell-DGE with microcapillary manipulation, a technique that can be used to analyze the gene expression of individual cells without detaching them from their tightly associated tissues, enabling us to retain positional information and investigate cell-cell interactions.

plant biology↗