Biology subjects

Imai, A.

Publications and source records attributed to Imai, A..

5 recordsLinked to original sources

bioRxiv2024

Comprehensive gene expression analysis of organoid-derived healthy human colonic epithelium and cancer cell line by stimulated with live probiotic bacteria

The large intestine has a dense milieu of indigenous bacteria, generating a complex ecosystem with crosstalk between individual bacteria and host cells. In vitro host cell modeling and bacterial interactions at the anaerobic interphase have elucidated the crosstalk molecular basis. Although classical cell lines derived from patients with colorectal cancer including Caco-2 cells are used, whether they adequately mimic normal colonic epithelial physiology is unclear. To address this, we performed transcriptome profiling of Caco-2 and Monolayer cells derived from healthy Human Colonic Organoid (MHCO) cultured hemi-anaerobically. Coculture with the anaerobic gut bacteria, Bifidobacterium longum subsp. longum differentiated the probiotic effects of test cells from those of physiologically normal intestinal and colorectal cancer cells. We cataloged non- or overlapping gene signatures where gene profiles of Caco-2 cells represented absorptive cells in the small intestinal epithelium, and MHCO cells showed complete colonic epithelium signature, including stem/progenitor, goblet, and enteroendocrine cells colonocytes. Characteristic gene expression changes related to lipid metabolism, inflammation, and cell-cell adhesion were observed in cocultured live Bifidobacterium longum and Caco-2 or MHCO cells. B. longum-stimulated MHCO cells exhibited barrier-enhancing characteristics, as demonstrated in clinical trials. Our data represent a valuable resource for understanding gut microbe and host cell communication.

ecology↗

bioRxiv2023

Impact of climate change and oligotrophication on quality and quantity of lake primary production: A case study in Lake Biwa

Global climate change and anthropogenic oligotrophication are expected to reshape the dynamics of primary production (PP) in aquatic ecosystems; however, few studies have explored their long-term effects. In theory, the PP of phytoplankton in Lake Biwa may decline over decades due to warming, heightened stratification, and anthropogenic oligotrophication. Furthermore, the PP of large phytoplankton, which are inedible to zooplankton, along with biomass-specific productivity (PBc), could decrease. In this study, data from 1976-2021 and active fluorometry measurements taken in 2020 and 2021 were evaluated. Quantitatively, the temporal dynamics of mean seasonal PP during 1971-2021 were assessed according to the carbon fixation rate to investigate relationships among environmental factors. Qualitatively, phytoplankton biomass, PP, and PBc were measured in two size fractions [edible (S) or inedible (L) for zooplankton] in 2020 and 2021, and the L:S balance for these three measures was compared between 1992 (low-temperature/high-nutrient conditions) and 2020-2021 (high-temperature/low-nutrient conditions) to assess seasonal dynamics. The results indicated that climate change and anthropogenic oligotrophication over the past 50 years have diminished Lake Biwas PP since the 1990s, impacting the phenology of PP dynamics. However, the L:S balance in PP and PBc has exhibited minimal change since 1992. These findings suggest that, although climate change and oligotrophication may reduce overall PP, they do not markedly alter the inedible/edible phytoplankton balance in terms of PP and PBc. Instead, as total PP declines, the production of small edible phytoplankton decreases proportionally, potentially affecting trophic transfer efficiency and material cycling in Lake Biwa.

ecology↗

bioRxiv2021

Size-dependent susceptibility of lake phytoplankton to light stress: An implication for succession of large green algae in a deep oligotrophic lake

Field observations of the population dynamics and measurements of photophysiology in Lake Biwa were conducted by size class (< vs. > 30 m) from early summer to autumn to investigate the relationships between susceptibility to light stress and cell size. Also, a nutrient bioassay was conducted to clarify whether the growth rate and photosystem II (PSII) photochemistry of small and large phytoplankton are limited by nutrient availability. Large phytoplankton, which have lower intracellular Chl-a concentrations, had higher maximum PSII photochemical efficiency (Fv/Fm) but lower non-photochemical quenching (NPQNSV) than small phytoplankton under both dark and increased light conditions. The nutrient bioassay revealed that the PSII photochemistry of small phytoplankton was restricted by N and P deficiency at the pelagic site even at the end of the stratification period, while that of large phytoplankton was not. These results suggest that large phytoplankton have lower susceptibility to PSII photodamage than small phytoplankton due to lower intracellular Chl-a concentrations. The size dependency of susceptibility to PSII photoinactivation may play a key role in large algal blooms in oligotrophic water.

microbiology↗

bioRxiv2020

Development of photosynthetic carbon fixation model using multi-excitation wavelength fast repetition rate fluorometry in Lake Biwa

Direct measurements of gross primary productivity (GPP) in the water column are essential, but can be spatially and temporally restrictive. Fast repetition rate fluorometry (FRRf) is a bio-optical technique based on chlorophyll a (Chl-a) fluorescence that can estimate the electron transport rate (ETRPSII) at photosystem II (PSII) of phytoplankton in real time. However, derivation of phytoplankton GPP in carbon units from ETRPSII remains challenging because the electron requirement for carbon fixation ([FE]e,C) can vary depending on multiple factors. Also, the FRRf is still relatively novel, especially in freshwater ecosystems where phosphorus limitation and cyanobacterial blooms are common. The goal of the present study is to construct a robust [FE]e,C model for freshwater ecosystems using simultaneous measurements of ETRPSII by FRRf with multi-excitation wavelengths coupled with traditional carbon fixation rate by the 13C method. The study was conducted in oligotrophic and mesotrophic areas in Lake Biwa from July 2018 to May 2019. The combination of excitation light at 444, 512 and 633 nm correctly estimated ETRPSII of cyanobacteria. The range of [FE]e,C in the phytoplankton community varied from 1.1 to 31.0 mol e- mol C-1 during the study period. Generalized liner model showed the best model including 12 physicochemical and biological factors explained 67% of the variance in [FE]e,C. Among all factors, water temperature was the most significant, while PAR intensity was not. The GPP values estimated by FRRf (GPPf) with the best [FE]e,C model relative to 13C (GPP13C) varied 0.5-1.5. Further, GPPf estimated with more parsimonious [FE]e,C models were also comparable to GPP13C. This study quantifies the applicability of the in situ FRRf methodology, and supports continuous monitoring of GPP by FRRf in lakes with large spatio-temporal variability of environmental conditions and phytoplankton assemblages.

microbiology↗

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↗