Biology subjects

Inoue, K.

Publications and source records attributed to Inoue, K..

6 recordsLinked to original sources

bioRxiv2018

The sunlit microoxic niche of the archaeal eukaryotic ancestor comes to light

Recent advances in phylogenomic analyses and increased genomic sampling of uncultured prokaryotic lineages brought compelling evidence in support of the emergence of eukaryotes from within the Archaea domain of life. The discovery of Asgardaeota archaea and their recognition as the closest extant relative of eukaryotes fuelled the revival of a decades-old debate regarding the topology of the tree of life. While it is apparent that Asgardaeota encode a plethora of eukaryotic-specific proteins (the highest number identified to date in prokaryotes), the lack of genomic information and metabolic characterization has precluded inferences about their lifestyles and the metabolic landscape that may have favoured the emergence of the hallmark eukaryotic subcellular architecture. Here, we use advanced phylogenetic analyses to infer the deep ancestry of eukaryotes and genome-scale metabolic reconstructions to shed light on the metabolic milieu of the closest archaeal eukaryotic ancestors discovered till date. In doing so, we: i) generate the largest Asgardaeota genomic dataset available so far, ii) describe a new clade of rhodopsins encoded within the recovered genomes, iii) provide unprecedented evidence for mixotrophy within Asgardaeota, iv) present first-ever proofs that the closest extant archaeal relatives to all eukaryotes (Heimdallarchaeia) have microoxic lifestyles with aerobic metabolic pathways unique among Archaea (i.e. kynurenine pathway) and v) generate the first images of Asgardaeota.

microbiology↗

bioRxiv2018

Monkey Features Location Identification Using Convolutional Neural Networks

Understanding animal behavior in its natural habitat is a challenging task. One of the primary step for analyzing animal behavior is feature detection. In this study, we propose the use of deep convolutional neural network (CNN) to locate monkey features from raw RGB images of monkey in its natural environment. We train the model to identify features such as the nose and shoulders of the monkey at about 0.01 model loss.

animal behavior and cognition↗

bioRxiv2018

Deletion of class II ARF causes essential tremors through Nav1.6 traffic impairment

ADP-ribosylation factors (ARFs) are a family of small monomeric GTPases consisting of three classes. In the present study, we generated class II ARF-deficient mice (ARF4+/-/ARF5-/-) and found that they exhibited severe movement-associated tremors. Treatment of the mice with propranolol and gabapentin, which alleviate symptoms in patients with essential tremors, similarly reduced the amplitude of the pathologic tremors. In vivo electrophysiological recordings of the ARF4+/-/ARF5-/- mice revealed that they exhibited reduced excitability of their cerebellar Purkinje cells. Immunohistochemical studies revealed that ARF4+/-/ARF5-/- mice exhibit a severe, selective reduction of Nav1.6 proteins that are important for maintaining repetitive action potential firing in the axon initial segments (AISs) of the Purkinje cells. This decrease in Nav1.6 protein expression and the consequent tremors were alleviated by Purkinje cell-specific expression of ARF5. These results indicate that class II ARF mediates the selective trafficking of Nav1.6 to the AISs in cerebellar Purkinje cells, and suggest that the essential tremors can be ascribed to the reduced intrinsic excitability of Purkinje cells, caused by the selective decrease of Nav1.6 proteins in the AISs.

neuroscience↗

bioRxiv2018

Heliorhodopsins are absent in diderm (Gram-negative) bacteria: Some thoughts and possible implications for activity

Microbial heliorhodopsins are a new type of rhodopsins with an opposite membrane topology compared to type-1 and -2 rhodopsins, currently believed to engage in light sensing. We determined their presence/absence is monoderms and diderms representatives from the Tara Oceans and freshwater 25 lakes metagenomes. Heliorhodopsins were absent in diderms, confirming our previous observations in cultured Proteobacteria. Based on these observations, we speculate on the putative role of heliorhodopsins in light-driven transport of amphiphilic molecules.

microbiology↗

bioRxiv2017

Toward Machine Learning-based Data-driven Functional Protein Studies: Understanding Colour Tuning Rules and Predicting the Absorption Wavelengths of Microbial Rhodopsins

The light-dependent ion-transport function of microbial rhodopsin has been widely used in optogenetics for optical control of neural activity. In order to increase the variety of rhodopsin proteins having a wide range of absorption wavelengths, the light absorption properties of various wild-type rhodopsins and their artificially mutated variants were investigated in the literature. Here, we demonstrate that a machine-learning-based (ML-based) data-driven approach is useful for understanding and predicting the light-absorption properties of microbial rhodopsin proteins. We constructed a database of 796 proteins consisting of microbial rhodopsin wildtypes and their variants. We then proposed an ML method that produces a statistical model describing the relationship between amino-acid sequences and absorption wavelengths and demonstrated that the fitted statistical model is useful for understanding colour tuning rules and predicting absorption wavelengths. By applying the ML method to the database, two residues that were not considered in previous studies are newly identified to be important to colour shift.

biophysics↗

bioRxiv2017

Glutamine metabolism regulates Th2 cell differentiation via the α-ketoglutarate-dependent demethylation of histone H3K27

The acquisition of T cell functions seems to be closely linked to the reprogramming of the metabolic pathway. However, the impact of metabolic changes on the differentiation of helper T cell subsets remains unclear. We found that TCR-mediated activation of glutamine metabolism regulates Th2 cell differentiation via the supplementation of -ketogulutalate (-KG) and histone H3K27 demethylation. Deprivation of glutamine or pharmacological inhibition of glutamine metabolism blocks the induction of Th2 cell differentiation without affecting Stat6 phosphorylation. The methylation status of H3K27 at the Th2 cytokine gene locus was significantly increased in Th2 cells cultured under glutamine-deprived conditions. The inhibitory effect of glutamine-deprivation was antagonized by -KG, and the -KG-dependent induction of Th2 cell differentiation was reduced in utx- and jmjd3-deficient naive CD4 T cells. These findings show that the glutamine-a-ketoglutarate axis is crucial to regulating the epigenetic status at the Th2 cytokine gene locus and subsequent Th2 cell differentiation.

immunology↗