Biology subjects

Ohta, Y.

Publications and source records attributed to Ohta, Y..

11 recordsLinked to original sources

bioRxiv2026

Cartilaginous fish inform the lineage-specific evolution and MHC association of the TLR family

Chondrichthyans (sharks, rays and chimaeras) diverged from other vertebrate lineages over 400 million years ago and possess fully functional innate and adaptive immune systems. They comprise over 1,200 species occupying diverse aquatic habitats, from fresh to marine waters and from shallow to deep seas. Exposure to diverse pathogens through time, together with contemporary ocean warming and habitat degradation driven by climate change, has likely shaped unique immune mechanisms in these species. Toll-like receptors (TLRs) are central components of innate immunity, recognizing conserved pathogen-associated molecular patterns and initiating immune responses, yet their diversity remains poorly characterized in Chondrichthyans. Here, we characterize the TLR gene repertoire in elasmobranchs (sharks and rays) using genomic and transcriptomic data. We identify orthologs spanning all known vertebrate TLR families, including genes shared with agnathans as well as gnathostome-specific genes, and detect lineage-specific patterns of TLR duplication and loss, particularly in squaliform sharks and rays. Molecular evolution analyses indicate that most elasmobranch TLRs are under strong purifying selection, with positively selected sites in all genes, consistent with ongoing adaptation to pathogen-and environment-driven pressures. Several TLRs co-localize with genomic regions enriched in immune genes, including MHC paralogous regions, suggesting an ancestral genomic hotspot for vertebrate immunity.

evolutionary biology↗

bioRxiv2025

Moderated designs can balance between batch-effect mitigation and cell loss due to hashtag-assisted pooling in single-cell experiments

Minimizing experimental noise is integral to robust data generation in single-cell science. Experimental processing of different samples as a single pool, made possible by hashtag-assisted pooling, helps minimize batch-effects, but the computational demultiplexing of the data can also lead to loss of cells whose hashtags cannot be resolved accurately. Here, we examine four alternate experimental designs that could be used instead of a single-pool approach and quantify the batch effects as well as cell loss in each case. While a reference design offers the best performance, this study can help individual investigators choose one suited for their biological questions.

bioinformatics↗

bioRxiv2024

Kinetic patterns of single cell gene expression discriminate between the murine cellular responses to live attenuated and inactivated Yellow Fever vaccines

The success of the live attenuated Yellow Fever vaccine (YF17D) that elicits immunity lasting over thirty years has made it a widely used model to understand the generation of durable protection. We compare the early single-cell level transcriptional response in mice to YF17D and an adjuvanted-inactivated, but less effective version (InYF). Within the first week, we identify 70 kinetic patterns in 45 cellular clusters, majority of which discriminate between the two formulations, some in a tissue and sex-specific manner. Intriguingly, differential transcripts fall into two categories, one whose association with YF17D or InYF is maintained even when decoupled from their cell-type of expression and the other where such cell-plus-gene pairing is critical to maintain differential marker status. We demonstrate applications of this resource, by identifying B cells with varied interferon and antigen responsiveness in relation to each vaccine. This high-resolution dataset is amenable to further biomarker discovery and hypothesis generation.

immunology↗

bioRxiv2024

CountASAP: A Lightweight, Easy to Use Python Package for Processing ASAPseq Data

Declining sequencing costs coupled with the increasing availability of easy-to-use kits for the isolation of DNA and RNA transcripts from single cells have driven a rapid proliferation of studies centered around genomic and transcriptomic data. Simultaneously, a wealth of new techniques have been developed that utilize single cell technologies to interrogate a broad range of cell-biological processes. One recently developed technique, transposase-accessible chromatin with sequencing (ATAC) with select antigen profiling by sequencing (ASAPseq), provides a combination of chromatin accessibility assessments with measurements of cell-surface marker expression levels. While software exists for the characterization of these datasets, there currently exists no tool explicitly designed to reformat ASAP surface marker FASTQ data into a count matrix which can then be used for these downstream analyses. To address this, we created CountASAP, an easy-to-use Python package purposefully designed to transform FASTQ files from ASAP experiments into count matrices compatible with commonly-used downstream bioinformatic analysis packages. CountASAP takes advantage of the independence of the relevant data structures to perform fully parallelized matches of each sequenced read to user-supplied input ASAP oligos and unique cell-identifier sequences.

bioinformatics↗

bioRxiv2023

MARK3-mediated Slingshot-1 phosphorylation is essential for polarized lamellipodium formation

Cofilin acts as a key regulator of actin cytoskeletal remodeling via stimulating actin filament disassembly. Cofilin is inactivated by Ser-3 phosphorylation and reactivated by cofilin-phosphatase Slingshot-1 (SSH1). SSH1 is activated upon binding to F-actin, and this activation is inhibited by its phosphorylation at Ser-937 and Ser-978 and the subsequent binding of 14-3-3 proteins. In this study, we identified MARK3 (also named Par-1a and C-TAK1) as a kinase responsible for Ser-937/Ser-978 phosphorylation of SSH1. MARK3-mediated phosphorylation promoted SSH1 binding to 14-3-3 proteins and suppressed its F-actin-assisted cofilin-phosphatase activity. When Jurkat cells were stimulated with SDF-1, actin filaments formed multidirectional F-actin-rich lamellipodia around the cells in the initial stage, and thereafter, they were rearranged as a single polarized lamellipodium to the direction of cell migration. Upon SDF-1 stimulation, SSH1 was translocated into F-actin-rich lamellipodia, but its Ser-937/Ser-978 non-phosphorylatable mutant SSH1(2SA) was retained at the location of the original cortical F-actin. Knockdown of MARK3 or overexpression of SSH1(2SA), similar to SSH1 knockdown, impaired the conversion of multiple lamellipodia to a single polarized lamellipodium. These results indicate that MARK3-mediated Ser-937/Ser-978 phosphorylation is required for SSH1 liberation from F-actin and translocation to lamellipodia, and hence, facilitates the formation of a single polarized lamellipodium for directional cell migration. Our results suggest that the phosphorylation-dephosphorylation cycle of SSH1 is crucial for its localization to lamellipodia via promoting the dissociation-reassociation cycle of SSH1 to F-actin, and thereby the stimulus-induced lamellipodium formation to the direction of cell movement.

cell biology↗

bioRxiv2021

Laboratory analysis of glucose, fructose, and sucrose contents in Japanese common beverages for the exact assessment of beverage-derived sugar intake

BackgroundThe adverse health effects of sugar-sweetened beverage consumption have been studied worldwide. There are several reports on actual sugar contents in sugar-sweetened beverages. However, there is no recent report on actual sugar contents in Japanese sugar-sweetened beverages. Therefore, we attempted to analyze glucose, fructose, and sucrose contents in Japanese common beverages. MethodsGlucose, fructose, and sucrose contents in 49 beverages including 8 energy drinks, 11 sodas, 4 fruit juices, 7 probiotic drinks, 4 sports drinks, 5 coffee drinks, 6 green tea drinks, and 4 tea drinks were determined using the enzymatic methods. ResultsTow zero calorie drinks, 2 sugarless coffee drinks, and 6 green tea drinks contained no sugar. Three coffee drinks contained only sucrose. The orders of median glucose, fructose, and sucrose contents in categorized beverages containing sugars were as follows: for glucose, fruit juice > energy drink [≥] soda >> probiotic drink > black tea drink > sports drink; for fructose, probiotic drink [≥] energy drink > fruit juice > soda >> sports drink > black tea drink; and for sucrose, black tea drink > energy drink [≥] probiotic drink > fruit juice > soda > coffee drink >> sports drink. The rate of total fructose content in total sugar content in 38 sugar-containing beverages was approximately 40-60%. The total sugar content analyzed was not always equivalent to carbohydrate content indicated on the nutrition label. ConclusionsThese results indicate that actual sugar content in Japanese common beverages is necessary for the exact assessment of beverage-derived sugar intake.

biochemistry↗

bioRxiv2020

Association between the extent of DNA methylation at the CpG sites of HIF3A and parameters of obesity in the general Japanese population

Obesity is a major public health problem worldwide owing to the substantial increase in risk of metabolic diseases. Hypoxia-inducible factors (HIFs) regulate transcriptional responses to hypoxic stress. DNA methylation in the CpG sites of intron 1 of HIF3A is associated with body mass index in the whole blood and adipose tissue. This study investigates the correlation between DNA methylation of HIF3A and parameters of obesity, including thickness of visceral (VAT) and subcutaneous adipose tissues, in the general Japanese population. Participants (220 men and 253 women) who underwent medical examination were enrolled in this cross-sectional study. We used pyrosequencing to quantify DNA methylation (CpG sites of cg16672562, cg22891070, and cg27146050) in HIF3A. DNA methylation of HIF3A was only different in women. Multiple regression analysis showed that DNA methylation level at cg27146050 was associated with thickness of VAT in women. DNA methylation level at cg27146050 also correlated with body mass index and percentage of body fat in women after excluding smokers and non-smokers who quit smoking with the last 5 years. DNA methylation in the CpG site (cg27146050) of HIF3A correlated with parameters of obesity in Japanese women.

biochemistry↗

bioRxiv2020

Cellular logics bringing the symmetry breaking in spiral nucleation revealed by trans-scale imaging

SummaryThe spiral wave is a commonly observed spatio-temporal order in diverse signal relaying systems. Although properties of generated spirals have been well studied, the mechanisms for their spontaneous generation in living systems remain elusive. By the newly developed imaging system for trans-scale observation of the intercellular communication among ∼130,000 cells of social amoeba, we investigated the onset dynamics of cAMP signaling and identified mechanisms for the self-organization of the spiral wave at three distinct scalings: At the population-level, the structured heterogeneity of excitability fragments traveling waves at its high/low boundary, that becomes the generic source of the spiral wave. At the cell-level, both the pacemaking leaders and pulse-amplifying followers regulate the heterogeneous growth of the excitability. At the intermediate-scale, the essence of the spontaneous wave fragmentation is the asymmetric positioning of the pacemakers in the high-excitability territories, whose critical controls are operated by a small number of cells, pulse counts, and pulse amounts.Competing Interest StatementThe authors have declared no competing interest.View Full Text

systems biology↗

bioRxiv2020

Feed restriction in mid-lactation dairy cows. II: Effects on protein metabolism-related blood metabolites.

The aim of the study was to describe the metabolic responses of protein metabolism to a period of negative nutrient balance induced by feed restriction (FR). Seven multiparous Holstein cows (93 ± 15 days in milk) were randomly assigned to 7 treatments in a 7 × 4 Youden square design. Daily intake was restricted to provide 60% of energy requirements during 5 d except for one treatment with ad libitum (AL) feeding. While 5 out of 7 experimental treatments involved abomasal supplementation of AA or glucose, in this article we evaluated only the effects of FR by comparing both control treatments (AL and FR). Data of 2 cows within the AL group were removed due to sickness and therefore it had n = 2. A rapid decrease of most amino acids in plasma was paired with an increase in blood urea N with its peak on d 2 and decreasing afterwards. On the other hand, Lys, Arg, Gly, Gln, and Cys were greater during FR. Comparing the fluctuation of all the essayed N components in circulation across the 5-d period, protein tissue mobilization may have supplied amino acids for catabolism to provide needs for N and energy precursors.Implications The short-term feed restriction model described in this article can serve as an alternative to study metabolic adaptations during the transition period. The response observed of the protein metabolism sets the baseline to measure the effect of nutrients supplementation and identify those candidates that will improve milk production and overall health after calving.Competing Interest StatementThe authors have declared no competing interest.View Full Text

physiology↗

bioRxiv2020

Feed restriction in mid-lactation dairy cows. I: Effects on milk production and energy metabolism-related blood metabolites.

The aim of the study was to describe the metabolic responses on energy metabolism to a period of negative nutrient balance induced by feed restriction (FR). Seven multiparous Holstein cows (93 ± 15 days in milk) were randomly assigned to 7 treatments in a 7 × 4 Youden square design. Daily intake was restricted to provide 60% of energy requirements during 5 d except for one treatment with ad libitum (AL) feeding. While 5 out of 7 experimental treatments involved abomasal supplementation of amino acids or glucose, in this article we evaluated only the effects of a negative nutrient balance by comparing both control treatments (AL and FR). Data of 2 cows within the AL group were removed due to sickness and therefore it had n = 2. Milk and energy corrected milk yield were reduced by FR. Yields of milk protein and lactose were lower during FR than during AL but the yield of milk fat only had a tendency (P > 0.06) to be lower with FR. Milk protein concentration was lower with FR than with AL but concentration of milk lactose and fat were not different between diets. The FR induced a decrease in plasma insulin and glucose concentrations, with quadratic decreasing trends both reaching nadirs on d 3. Simultaneously, non-esterified fatty acids (NEFA) concentration was greater and increased quadratically, peaking at d 3 during FR. There were no differences in daily β-hydroxybutyrate concentration, but it increased linearly until d 4 with FR. Comparison of the variation in concentration after feeding of insulin, NEFA and glucose could indicate a likely increased insulin sensitivity for peripheral NEFA uptake and a resistance for glucose uptake. This mechanism would contribute to decrease NEFA in circulation and sparing of glucose for lactose synthesis, respectively. Metabolic adaptations to a short-term reduction in dry matter intake include lipid mobilization, as well as modulation of peripheral tissue endocrine sensitivity in order to maintain yield of milk components production but prioritizing milk fat and lactose over milk protein.Implications The short-term feed restriction model described in this article can serve as an alternative to study metabolic adaptations during the transition period. The response of energy metabolism observed sets the baseline to measure the effect of nutrients supplementation and identify those candidates that will improve milk production and overall health after calving.Competing Interest StatementThe authors have declared no competing interest.View Full Text

physiology↗

bioRxiv2020

LSD1 represses a neonatal/reparative gene program in adult intestinal epithelium

Intestinal epithelial homeostasis is maintained by adult intestinal stem cells, which, alongside Paneth cells, appear after birth in the neonatal period. We aimed to identify new regulators of neonatal intestinal epithelial development by testing a small library of epigenetic modifier inhibitors in Paneth cell-skewed organoid cultures. We found that Lysine-specific demethylase 1A (Kdm1a/Lsd1) is absolutely required for Paneth cell differentiation. Lsd1-deficient crypts, devoid of Paneth cells, are still able to form organoids without a requirement of exogenous or endogenous Wnt. Mechanistically, we find that LSD1 represses genes that are normally expressed in fetal and neonatal epithelium. This gene profile is similar to what is seen in repairing epithelium, and indeed, we find that Lsd1-deficient epithelium has superior regenerative capacities after irradiation injury. In summary, we found an important regulator of neonatal intestinal development and identified a druggable target to reprogram intestinal epithelium towards a reparative state.

developmental biology↗