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Biology subjects

Yagi, Y.

Publications and source records attributed to Yagi, Y..

4 recordsLinked to original sources

Analysis of oogenesis defects in Dyro mutant of Drosophila melanogaster.

Dyro mutant is female sterile, and oogenesis is aborted during stage8-9 of oogenesis. We investigated detail of the oogenesis defect of Dyro mutant. At first, we confirmed loss of Dyro caused female sterility by genetic rescue experiment. Then, we performed genetic mosaic analysis and found Dyro expression in germ cell is important for oogenesis. In Dyro mutant, inhibition of programmed cell death suppressed cell death of germ cells during oogenesis but failed to rescue fertility. It indicates that abortion of oogenesis is not because of mis-regulation of cell death signal but there is oogenesis defect which activates Caspase signaling pathway. Then, we observed Dyro mutant and looking for defects which may trigger cell death of germ cells in Dyro mutant. We found oogenesis abortion timing is similar to yolk protein mutant but different from amino acid starvation. It suggests that nutrient signal defect does not triggers cell death in Dyro mutant. We carefully observed the defect of Dyro mutant ovaries and found abnormal morphology of nucleolus and chromosome in nurse cells. It seems chromosome in Dyro mutant is thick and nucleolus is limited in small space between thick chromosomes in Dyro mutant nurse cells. Other defect we found is aggregated protein accumulation in germ cells. These data suggest that Dyro has important role in mid-oogenesis stage germ cell and loss of Dyro causes defect in nuclear of nurse cells which may leads to abortion of oogenesis.

developmental biology↗

Spatio-temporal model and machine learning method reveal process of phenological shift under climate change of North Pacific spiny dogfish

Climate change has disrupted natural phenological patterns, including migration. Despite extensive studies of phenological shifts in migration by climate change and driving factors of migration, a few issues remain unresolved. In particular, little is known about the complex effects of driving factors on migration with interactions and nonlinearity, and partitioning of the effects of factors into spatial, temporal, and spatio-temporal effects. The Pacific spiny dogfish Squalus suckleyi (hereafter "spiny dogfish") is a coastal elasmobranchii that migrates southward for parturition and northward for feeding in the western North Pacific. Here, to elucidate the migration patterns as well as the driving factors under climate change, we first examined long-term changes in the timing and geographic location of migration by applying a spatio-temporal model to ca. 5-decade time series data for the presence/absence of spiny dogfish in the western North Pacific. We then evaluated the spatial, temporal, and spatio-temporal effects of driving factors (sea surface temperature [SST], depth, productivity, and magnetic fields) on seasonal occurrence patterns using a machine learning model. We found that the migration area did not change over ca. 5 decades, whereas the migration timing advanced by a month after 2000. The spatial effects of magnetic fields and depth were consistently large and the spatial and spatio-temporal effects of SST increased in the migration season, even though temporal effect of SST was always weak. These results suggest that the migration area of spiny dogfish was stable over time because their spatial distribution was determined by geographic features, whereas the migration timing advanced by tracking a suitable SST location which increased steeply after 2000. Therefore, temperature as well as other factors influence migration simultaneously under climate change and underline the importance of paying attention biotic/abiotic factors including temperature and process-based understanding to predict future impacts of climate change on phenological shifts.

ecology↗

Identification of bacterial drug-resistant cells by the convolutional neural network in transmission electron microscope images

The emergence of bacteria that are resistant to antibiotics is common in areas where antibiotics are used widely. The current standard procedure for detecting bacterial drug resistance is based on bacterial growth under antibiotic treatments. Here we describe the morphological changes in enoxacin-resistant Escherichia coli cells and the computational method used to identify these resistant cells in transmission electron microscopy (TEM) images without using antibiotics. Our approach was to create patches from TEM images of enoxacin-sensitive and enoxacin-resistant E. coli strains, use a convolutional neural network for patch classification, and identify the strains on the basis of the classification results. The proposed method was highly accurate in classifying cells, achieving an accuracy rate of 0.94. Using a gradient-weighted class activation mapping to visualize the region of interest, enoxacin-resistant and enoxacin-sensitive cells were characterized by comparing differences in the envelope. Moreover, Pearsons correlation coefficients suggested that four genes, including lpp, the gene encoding the major outer membrane lipoprotein, were strongly associated with the image features of enoxacin-resistant cells.

systems biology↗

Requirement for proper mitochondrial RNA processing in the restrictive control of cell proliferation during early lateral root morphogenesis

Although mechanisms that activate organogenesis in plants are well established, much less is known about the subsequent fine-tuning of cell proliferation, which is crucial for creating properly structured and sized organs. Here we show, through analysis of temperature-dependent fasciation (TDF) mutants of Arabidopsis, root redifferentiation defective 1 (rrd1), rrd2, and root initiation defective 4 (rid4), that mitochondrial RNA processing is required for limiting cell division during early lateral root (LR) organogenesis. These mutants formed abnormally broadened (i.e., fasciated) LRs under high-temperature conditions due to excessive cell division. All TDF proteins localized to mitochondria, where they were found to participate in RNA processing: RRD1 in mRNA deadenylation, and RRD2 and RID4 in mRNA editing. Further analysis suggested that LR fasciation in the TDF mutants is triggered by reactive oxygen species generation caused by defective mitochondrial respiration. Our findings provide novel clues for the physiological significance of mitochondrial activities in plant organogenesis.

plant biology↗