Biology subjects

Koyama, Y.

Publications and source records attributed to Koyama, Y..

5 recordsLinked to original sources

bioRxiv2025

f4-statistics-based ancestry profiling and convolutional neural network phenotyping shed new light on the structure of genetic and spike shape diversity in Aegilops tauschii Coss.

Aegilops tauschii Coss., a progenitor of bread wheat, is an important wild genetic resource for breeding. The species comprises three genetically defined lineages (TauL1, TauL2, and TauL3), each displaying distinctive phenotypes in various agronomic traits, including spike shape. In the present work, we studied the relationship between population structure and spike shape variation patterns using a collection of 249 accessions. f4-statistics-based ancestry profiling confirmed the previously identified lineages and revealed a genetic component derived from TauL3 in the genomes of some southern Caspian and Transcaucasus TauL1 and TauL2 accessions. Spike shape variation patterns were analyzed using a convolutional neural network-based approach, trained on green and dry spike image datasets. This analysis showed that spike shape diversity is structured according to lineages and demonstrated that the lineages can be distinguished based on spike shape. The implications of these findings for the origins of common wheat and the intraspecific taxonomy of Ae. tauschii are discussed. Plain Language SummaryWild wheat, Aegilops tauschii, represents a vast reservoir of alleles that have not yet been utilized in breeding. These alleles may confer beneficial phenotypes, such as drought tolerance and disease resistance, when introduced into bread wheat. To fully leverage this reservoir, it is essential to quickly identify strains with potentially useful alleles. In Ae. tauschii, which consists of strain groups (lineages) with unique genetic makeups, this can be done by determining a strains lineage based on spike shape. In this work, we trained machine learning models for this purpose and found that spike shape diversity reflects lineage structure. These models demonstrated potential for practical use in assigning strains to their respective lineages based on spike shape. Our work opens new avenues for the application of machine learning in wheat improvement, as well as in the genetic and evolutionary studies of wheat morphology.

evolutionary biology↗

bioRxiv2024

Dynamic cognitive differences between internal and external attention are associated with depressive and anxiety disorders

The internal/external attention framework characterises attention focused on internal representations, such as emotions, versus external representations, such as perceptual stimuli. The inability to focus ones attention is considered a critical factor in psychiatric disorders. While these different attentional foci are likely generated by the dynamic interplay of multiple cognitive processes, previous studies have generally examined single cognitive dimensions. We developed a new method, cognitive dynamic similarity analysis (C-DSA), to clarify how cognitive processes differ between experimental conditions. In an MR scanner, participants performed a word-processing task in which they focused on either their own emotions or the number of letters associated with a stimulus. To extract cognitive dynamics at the single-trial level, we applied cognitive dynamics estimation, a recently developed method that generates whole-brain activation maps for four cognitive dimensions (emotion processing, selective attention, self-referential thought, and working memory) using a meta-analytic platform. We then performed C-DSA to calculate the difference between internal and external attention for each cognitive dimension. C-DSA revealed significant differences between internal/external attention in all cognitive dimensions, but especially in emotion processing. Moreover, the difference between attention conditions of selective attention was negatively associated with the severity of depression and state-anxiety, but positively associated with trait-anxiety. Our findings suggest that C-DSA applies to both naturalistic and controlled dynamic processes and may be valuable in clinical settings by linking dynamic cognitive mechanisms with issues like ageing and psychiatric disorders. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=174 SRC="FIGDIR/small/615274v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@1a1bbb4org.highwire.dtl.DTLVardef@12a587forg.highwire.dtl.DTLVardef@1181b45org.highwire.dtl.DTLVardef@1a6716c_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2023

Cognitive Dynamics Estimation: A whole-brain spatial regression paradigm for extracting the temporal dynamics of cognitive processes

Functional MRI (fMRI) has been instrumental in understanding how cognitive processes are spatially mapped in the brain, yielding insights about brain regions and functions. However, in case the orthogonality of behavioral or stimulus timing is not guaranteed, the estimated brain maps fail to dissociate each cognitive process, and the resultant maps become unstable. Also, the brain mapping exercise can not provide temporal information on the cognitive process. Here we propose a qualitatively different approach to fMRI analysis, named Cognitive Dynamics Estimation (CDE), that estimates how multiple cognitive processes change over time even when behavior or stimulus logs are unavailable. This method transposes the conventional brain mapping; the brain activity pattern at each time point is subject to regression analysis with data-driven maps of cognitive processes as regressors, resulting in the time series of cognitive processes. The estimated time series captured the fluctuation of intensity and timing of cognitive processes on a trial-by-trial basis, which conventional analysis could not capture. Notably, the estimated time series predicted participants cognitive ability to perform each psychological task. As an addition to our fMRI analytic toolkit, these results suggest the potential for CDE to elucidate underexplored cognitive phenomena, especially in the temporal domain. HighlightsWe propose a novel fMRI analysis that are equivalently effective to the brain mapping approach The temporal dynamics of multiple cognitive processes were captured on a trial-by-trial basis. This analysis can be applied data-driven even when the researchers do not have any hypothesis about what kind of cognitive processes are recruited in the task. This analysis can be applied even when the cognitive processes are strongly correlated in the temporal domain. The estimated temporal dynamics well predicted individuals cognitive ability required for each task.

neuroscience↗

bioRxiv2021

Regulation of gliotoxin biosynthesis and protection in Aspergillus species

Aspergillus fumigatus causes a range of human and animal diseases collectively known as aspergillosis. A. fumigatus possesses and expresses a range of genetic determinants of virulence, which facilitate colonisation and disease progression, including the secretion of mycotoxins. Gliotoxin (GT) is the best studied A. fumigatus mycotoxin with a wide range of known toxic effects that impair human immune cell function. GT is also highly toxic to A. fumigatus and this fungus has evolved self-protection mechanisms that include (i) the GT efflux pump GliA, (ii) the GT neutralising enzyme GliT, and (iii) the negative regulation of GT biosynthesis by the bis-thiomethyltransferase GtmA. The transcription factor (TF) RglT is the main regulator of GliT and this GT protection mechanism also occurs in the non-GT producing fungus A. nidulans. However, the A. nidulans genome does not encode GtmA and GliA. This work aimed at analysing the transcriptional response to exogenous GT in A. fumigatus and A. nidulans, two distantly related Aspergillus species, and to identify additional components required for GT protection. RNA-sequencing shows a highly different transcriptional response to exogenous GT with the RglT-dependent regulon also significantly differing between A. fumigatus and A. nidulans. However, we were able to observe homologs whose expression pattern was similar in both species (43 RglT-independent and 11 RglT-dependent). Based on this approach, we identified a novel RglT-dependent methyltranferase, MtrA, involved in GT protection. Taking into consideration the occurrence of RglT-independent modulated genes, we screened an A. fumigatus deletion library of 484 transcription factors (TFs) for sensitivity to GT and identified 15 TFs important for GT self-protection. Of these, the TF KojR, which is essential for kojic acid biosynthesis in Aspergillus oryzae, was also essential for virulence and GT biosynthesis in A. fumigatus, and for GT protection in A. fumigatus, A. nidulans, and A. oryzae. KojR regulates rglT, gliT, gliJ expression and sulfur metabolism in Aspergillus species. Together, this study identified conserved components required for GT protection in Aspergillus species. Author SummaryA. fumigatus secretes mycotoxins that are essential for its virulence and pathogenicity. Gliotoxin (GT) is a sulfur-containing mycotoxin, which is known to impair several aspects of the human immune response. GT is also toxic to different fungal species, which have evolved several GT protection strategies. To further decipher these responses, we used transcriptional profiling aiming to compare the response to GT in the GT producer A. fumigatus and the GT non-producer A. nidulans. This analysis allowed us to identify additional genes with a potential role in GT protection. We also identified 15 transcription factors (TFs) encoded in the A. fumigatus genome that are important for conferring resistance to exogenous gliotoxin. One of these TFs, KojR, which is essential for A. oryzae kojic acid production, is also important for virulence and GT protection in A. fumigatus, A. nidulans and A. oryzae. KojR regulates the expression of another TF, an oxidoreductase, previously shown to be essential for GT protection, and sulfur metabolism. Together, this work identified conserved components required for gliotoxin protection in Aspergillus species.

microbiology↗

bioRxiv2018

Structural basis for activation of Dot1L methyltransferase on the nucleosome by histone H2BK120 ubiquitylation

Histone H3 lysine 79 (H3K79) methylation is enriched on actively transcribed genes, and its misregulation is a hallmark of leukemia. Methylation of H3K79, which resides on the structured disk face of the nucleosome, is mediated by the Dot1L methyltransferase. Dot1L activity is part of a trans-histone crosstalk pathway, requiring prior histone H2B ubiquitylation of lysine 120 (H2BK120ub) for optimal activity. However, the molecular details describing both how Dot1L binds to the nucleosome and why Dot1L is activated by H2BK120 ubiquitylation are unknown. Here we present the cryo-EM structure of Dot1L bound to a nucleosome reconstituted with a site-specifically ubiquitylated H2BK120. The structure reveals that Dot1L engages the nucleosome acidic patch using an arginine anchor and occupies a conformation poised for methylation. Ubiquitin directly interacts with Dot1L and is positioned as a clamp on the nucleosome interacting region of Dot1L. Using our structure, we identify point mutations that disrupt the nucleosome-specific and ubiquitin-dependent activities of Dot1L. This study establishes a path to better understand Dot1L function in normal and leukemia cells.

biophysics↗