Biology subjects

Koyama, K.

Publications and source records attributed to Koyama, K..

8 recordsLinked to original sources

bioRxiv2025

Differential effects of the D1/S264V mutation in Photosystem II with either PsbA1 or PsbA3 on QB, non-heme Iron, and the associated hydrogen-bond network

The role of the D1/S264 residue and the role of its environment in the proton-coupled electron transfer reaction on the acceptor side of Photosystem II were investigated. To this end, D1/S264V mutants were constructed in the thermophilic cyanobacterium Thermosynechococcus elongatus, with D1 being either PsbA1 or PsbA3. The PSII mutants were investigated using EPR spectroscopy, thermoluminescence, (time-resolved) absorption changes measurements, and oximetry. While the mutation had minor effects in PsbA1-PSII, the S264V mutation in PsbA3-PSII had significant consequences: i) thermoluminescence data show inefficient electron transfer from QA- to QB; ii) re-oxidation of QA- was slowed, by at least a factor of 10; iii) the herbicides inhibit weakly O2 evolution; iv) no Fe2+QB- EPR signal was detected in dark-adapted PSII; instead, v) a large Fe3+ signal was present with vi) modified EPR properties; vii) no QA-Fe2+QB- biradical signal was observed after illumination at 198 K following a flash illumination, confirming the inefficient formation of QB-; viii) either no proton uptake coupled to non-heme iron reduction occurred or with a very slow rate compared to PsbA3-PSII; ix) changes were noted in the electrochromic response associated with QA- formation; and x) increased production of singlet oxygen, both with and without herbicides. The S264V mutation in PsbA3-PSII leads to a significant decrease in the energy gap between the QA-QB and QAQB- states. The effects listed above are discussed regarding the differences between PsbA1-PSII and PsbA3-PSII as those related to the sulfoquinovosyldiacylglycerol, the water molecules and the H-bond network.

biophysics↗

bioRxiv2024

Comparative analysis based on shared amplicon sequence variants reveals that cohabitation influences gut microbiota sharing between humans and dogs

IntroductionThe One Health concept is a comprehensive understanding of the interaction between humans, animals, and the environment. The cohabitation of humans and dogs positively affects their physical, mental, and social well-being. It is recognized as an essential factor from the One Health perspective. Furthermore, a healthy balance in the gut microbiome is essential for good health, and the sharing of gut microbes between humans and dogs may positively impact the health of both hosts. Therefore, elucidating the sharing of gut bacteria between humans and dogs is important for understanding One Health. However, most studies have examined sharing at the taxonomic level, and it remains unclear whether the same bacteria are transferred between humans and dogs, and whether they mutually influence each other. MethodsHere, microbiome analysis and 16S rRNA gene amplicon sequence variant (ASV) analysis was performed to address this question. Results16S rRNA gene ASVs analysis indicated that gut microbes have been transferred between humans and dogs. The overall structure of the gut microbiota within human-dog pairs remained unchanged after three months of adaptation. However, some ASVs were shared within human-dog pairs. Many shared ASVs were highly abundant within each host, and this high abundance may be considered a factor that influences bacterial transfer between hosts. DiscussionOur results demonstrate the possibility of the direct transfer of gut bacteria between humans and dogs, providing an important insight for achieving good health through human-dog cohabitation.

microbiology↗

bioRxiv2023

Beacon-based sleep status and physical activity monitoring in humans.

One out of every five people in Japan is dissatisfied with their sleep and various diseases caused by lack of exercise have been pointed out, but there are few effective remedies for these problems. In this study, we aimed to develop a simple method for measuring behavioral sleep patterns and physical activity using a beacon accelerometer wirelessly connected with a smartphone. A sleep prediction model was created comparing the data obtained from the accelerometer with the sleep status data obtained by a previously validated sleep monitoring system. The Random Forest model was able to classify sleep and wakefulness with a 97.4% and 85.4% precision, respectively, which were comparable to those of conventional acceleration-based sleep monitoring devices. Additionally, the same data acquisition method was used to classify exercise intensity into seven levels and a high correlation (r=0.813, p<0.0001) was found when comparing the classified exercise intensity to metabolic equivalent (MET) values. This suggests that the proposed method can be used for accurate measurement of both behavioral sleep and physical activity classifying over a long period of time.

physiology↗

bioRxiv2023

An attention network for predicting T cell receptor-peptide binding can associate attention with interpretable protein structural properties

Understanding how a T cell receptor (TCR) recognizes its specific ligand peptide is crucial for gaining insight into biological functions and disease mechanisms. Despite its importance, experimentally determining TCR-peptide interactions is expensive and time-consuming. To address this challenge, computational methods have been proposed, but they are typically evaluated by internal retrospective validation only, and few have incorporated and tested an attention layer from language models into structural information. Therefore, in this study, we developed a machine learning model based on a modified version of the Transformer, a source-target-attention neural network, to predict TCR-peptide binding solely from the amino acid sequences of the TCRs complementarity-determining region (CDR) 3 and the peptide. This model achieved competitive performance on a benchmark dataset of TCR-peptide binding, as well as on a truly new external dataset. Additionally, by analyzing the results of binding predictions, we associated the neural network weights with protein structural properties. By classifying the residues into large and small attention groups, we identified statistically significant properties associated with the largely attended residues, such as hydrogen bonds within the CDR3. The dataset that we have created and our models ability to provide an interpretable prediction of TCR-peptide binding should increase our knowledge of molecular recognition and pave the way to designing new therapeutics.

bioinformatics↗

bioRxiv2021

The scaffold-dependent function of RIPK1 in dendritic cells promotes injury-induced colitis

Receptor interacting protein kinase 1 (RIPK1) is a cytosolic multidomain protein that controls cell life and death. While RIPK1 promotes cell death through its kinase activity, it also functions as a scaffold protein to promote cell survival by inhibiting FADD-caspase 8-dependent apoptosis and RIPK3-MLKL-dependent necroptosis. This pro-survival function is highlighted by excess cell death and a perinatal lethality in Ripk1-/- mice. Recently, loss of function mutation of RIPK1 was found in patients with immunodeficiency and inflammatory bowel diseases. Hematopoietic stem cell transplantation restored not only immunodeficiency but also intestinal inflammatory pathology, indicating that RIPK1 in hematopoietic cells is critical to maintain intestinal immune homeostasis. Here, we generated dendritic cell (DC)-specific Ripk1-/- mice in a genetic background with loss of RIPK1 kinase activity and found that the mice developed spontaneous colonic inflammation characterized by increased neutrophil infiltration. In addition, these mice were highly resistant to injury-induced colitis. The increased neutrophil infiltration in the colon and the resistance to colitis were restored by dual inactivation of RIPK3 and FADD, but not by inhibition of RIPK3, MLKL, or ZBP1 alone. Altogether, these results reveal a scaffold activity-dependent role of RIPK1 in protecting colonic DCs from apoptotic insults and maintenance of colonic immune homeostasis.

immunology↗

bioRxiv2021

Prevalence of floating toe and its relationship with static postural stability in children: The Yamanashi adjunct study of the Japan Environment and Childrens Study (JECS-Y)

Floating toe (FT) is a frequently seen condition in which a toe is inadequately in contact with the ground. Although toes play an important role in stabilizing standing posture and walking, many aspects of the effects of FT on the body remain unclear. To our knowledge, there have been no reports about the relationship between FT and postural stability, especially in children. This study aimed to clarify the prevalence of FT and its relationship with static postural stability in children. Of the 400 children aged 8 years who participated in our cohort study, 396, who were examined for static postural stability, were included in this study. Postural stability and FT were assessed using a foot pressure plate. The sway path length of the center of pressure and the area of the ellipse defined as the size of the area marked by the center of pressure were measured as an evaluation of static postural stability. We calculated the "floating toe score (FT score: small FT score indicates insufficient ground contact of the toes)" using the image of the plantar footprint obtained at the postural stability measurement. The FT rate was very high at more than 90%, and the FT score in the eyes-closed condition was significantly higher than that in the eyes-open condition in both sexes. The FT score significantly correlated with the center of pressure path and area. Our results suggest that ground contact of the toes is not directly related to static postural stability in children, but it may function to stabilize the body when the condition becomes unstable, such as when the eyes are closed.

physiology↗

bioRxiv2019

Migratory divides coincide with species barriers across replicated avian hybrid zones above the Tibetan Plateau

Migratory divides are proposed to be catalysts for speciation across a diversity of taxa. However, the relative contribution of migratory behavior to reproductive isolation is difficult to test. Comparing reproductive isolation in hybrid zones with and without migratory divides offers a rare opportunity to directly examine the contribution of divergent migratory behavior to reproductive barriers. We show that across replicate sampling transects of two pairs of barn swallow (Hirundo rustica) subspecies, strong reproductive isolation coincided with an apparent migratory divide spanning 20 degrees of latitude. A third subspecies pair exhibited no evidence for a migratory divide and hybridized extensively. Within migratory divides, migratory phenotype was associated with assortative mating, implicating a central contribution of divergent migratory behavior to reproductive barriers. The remarkable geographic coincidence between migratory divides and genetic breaks supports a longstanding hypothesis that the Tibetan Plateau is a substantial barrier contributing to the diversity of Siberian avifauna.

evolutionary biology↗

bioRxiv2018

The potential aroma and flavor compounds in Vitis sp. cv. Koshu and V. vinifera L. cv. Chardonnay under different environmental conditions

ABSTRACTO_ST_ABSBACKGROUNDC_ST_ABSKoshu, a hybrid of Vitis vinifera L. and V. davidii Foex, is the most popular indigenous cultivar for wine production in Japan. However, little is known about the potential aroma compounds it contains and how environmental factors affect these. In this study, we obtained comprehensive profiles of the volatile (both glycosidically bound and free) and phenolic compounds that occur in Koshu berries, and compared these with similar profiles for V. vinifera cv. Chardonnay. We then compared the response of these two cultivars to bunch shading and the ripening-related phytohormone abscisic acid (ABA).\n\nRESULTSKoshu berries contained significantly higher concentrations of phenolic compounds, hydroxycinnamic acid derivatives, and some volatile phenols, such as 4-vinyl guaiacol and eugenol, than Chardonnay berries, which are thought to contribute to the characteristics of Koshu wine. In addition, Koshu berries had a distinctly different terpenoid composition from Chardonnay berries. Shading reduced the concentrations of norisoprenoid in both cultivars, as well as several phenolic compounds particularly their volatile derivatives in Koshu. The exogenous application of ABA induced ripening and increased the concentrations of lipid derivatives, such ashexanol, octanol, nonanol, and 1-octen-3-ol. Linear discriminant analysis showed that the aromatic potential could be discriminated clearly based on cultivar, bunch shading, and ABA application.\n\nCONCLUSIONThe unique secondary metabolite profiles of Koshu and their different responses to environmental factors could be valuable for developing various styles of Koshu wines and new cultivars with improved quality and cultural characteristics.

plant biology↗