Biology subjects

Mamiya, A.

Publications and source records attributed to Mamiya, A..

7 recordsLinked to original sources

bioRxiv2026

L3R-seq: A long-read 3'RACE approach for deep quantitative analysis of RNA processing

Long-read sequencing technologies offer the potential to capture multiple RNA processing events within single molecules, but standard protocols suffer from quantification biases and sequencing errors that limit their utility for precise analysis. Here, we describe Long-read 3 RACE-seq (L3R-seq), a targeted long-read sequencing method that ligates a unique molecular identifier (UMI)-containing adapter to the 3 end of RNA molecules prior to reverse transcription and PCR amplification. By grouping cDNA reads sharing the same UMI and generating a consensus sequence for each original RNA molecule, L3R-seq corrects random sequencing errors and mitigates PCR-duplicate-driven quantification biases. The method enables simultaneous, per-molecule analysis of RNA editing, 3 end cleavage and trimming, and polyadenylation status. Along with a step-by-step protocol for library preparation and sequencing with the Oxford Nanopore Technologies (ONT) platform, we describe an accompanying bioinformatic pipeline for consensus generation and extraction of RNA features. As an example, we apply L3R-seq to the mitochondrial mRNA ccmC from Arabidopsis thaliana, a transcript subject to extensive C-to-U editing and non-canonical 3 end processing. The workflow is readily adaptable to other RNAs targets and is transferable to the Pacific Biosciences (PacBio) platform.

bioinformatics↗

bioRxiv2025

Ascending nociceptive pathways drive rapid escape and sustained avoidance in adult Drosophila

Nociception -- the detection of harmful stimuli by the nervous system -- contributes to both rapid escape and long-term avoidance behaviors. Drosophila larvae detect damaging heat, mechanical, and chemical stimuli with specialized multidendritic (md) neurons, and these cells are among the only sensory neurons that survive metamorphosis. However, it remains unknown which somatosensory neurons contribute to nociception in adult flies. In an optogenetic screen, we found that abdominal md neurons were the only somatosensory class to induce rapid escape and sustained place avoidance. Calcium imaging from abdominal md axons revealed that they are activated by thermal nociceptive stimuli (>40{degrees}C). Connectomic reconstruction showed that md axons form their strongest synaptic connections with ascending interneurons that project to the brain. Among these, we identified two classes of ascending neurons that mediate rapid escape responses and a third that supports sustained avoidance. Our findings reveal that adult Drosophila meet several core criteria commonly used to define pain: dedicated nociceptors, ascending pathways connecting peripheral sensors to integrative brain centers, and a capacity for sustained avoidance of noxious stimuli.

neuroscience↗

bioRxiv2022

Biomechanical origins of proprioceptive maps in the Drosophila leg

Our ability to sense and move our bodies relies on proprioceptors, sensory neurons that detect mechanical forces within the body. Proprioceptors are diverse: different subtypes detect different features of joint kinematics, such as position, directional movement, and vibration. However, because they are located within complex and dynamic peripheral tissues, the underlying mechanisms of proprioceptor feature selectivity remain poorly understood. Here, we investigate molecular and biomechanical contributions to proprioceptor diversity in the Drosophila leg. Using single-nucleus RNA sequencing, we found that different proprioceptor subtypes express similar complements of mechanosensory and other ion channels. However, anatomical reconstruction of the proprioceptive organ and connected tendons revealed major biomechanical differences between proprioceptor subtypes. We constructed a computational model of the proprioceptors and tendons, which identified a putative biomechanical mechanism for joint angle selectivity. The model also predicted the existence of a goniotopic map of joint angle among position-tuned proprioceptors, which we confirmed using calcium imaging. Our findings suggest that biomechanical specialization is a key determinant of proprioceptor feature selectivity in Drosophila. More broadly, our discovery of proprioceptive maps in the fly leg reveals common organizational principles between proprioception and other topographically organized sensory systems.

neuroscience↗

bioRxiv2021

Functional architecture of neural circuits for leg proprioception in Drosophila

To effectively control their bodies, animals rely on feedback from proprioceptive mechanosensory neurons. In the Drosophila leg, different proprioceptor subtypes monitor joint position, movement direction, and vibration. Here, we investigate how these diverse sensory signals are integrated by central proprioceptive circuits. We find that signals for leg joint position and directional movement converge in second-order neurons, revealing pathways for local feedback control of leg posture. Distinct populations of second-order neurons integrate tibia vibration signals across pairs of legs, suggesting a role in detecting external substrate vibration. In each pathway, the flow of sensory information is dynamically gated and sculpted by inhibition. Overall, our results reveal parallel pathways for processing of internal and external mechanosensory signals, which we propose mediate feedback control of leg movement and vibration sensing, respectively. The existence of a functional connectivity map also provides a resource for interpreting connectomic reconstruction of neural circuits for leg proprioception.

neuroscience↗

bioRxiv2020

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↗

bioRxiv2020

Zero-determinant strategies under observation errors in repeated games

Zero-determinant (ZD) strategies are a novel class of strategies in the repeated prisoners dilemma (RPD) game discovered by Press and Dyson. This strategy set enforces a linear payoff relationship between a focal player and the opponent regardless of the opponents strategy. In the RPD game, games with discounting and observation errors represent an important generalization, because they are better able to capture real life interactions which are often noisy. However, they have not been considered in the original discovery of ZD strategies. In some preceding studies, each of them has been considered independently. Here, we analytically study the strategies that enforce linear payoff relationships in the RPD game considering both a discount factor and observation errors. As a result, we first reveal that the payoffs of two players can be represented by the form of determinants as shown by Press and Dyson even with the two factors. Then, we search for all possible strategies that enforce linear payoff relationships and find that both ZD strategies and unconditional strategies are the only strategy sets to satisfy the condition. We also show that neither Extortion nor Generous strategies, which are subsets of ZD strategies, exist when there are errors. Finally, we numerically derive the threshold values above which the subsets of ZD strategies exist. These results contribute to a deep understanding of ZD strategies in society.

animal behavior and cognition↗

bioRxiv2018

Neural coding of leg proprioception in Drosophila

Animals rely on an internal sense of body position and movement to effectively control motor behavior. This sense of proprioception relies on diverse populations of mechanosensory neurons distributed throughout the body. However, little is known about how proprioceptor neurons collectively encode sensory stimuli. Here, we investigate neural coding of leg proprioception in Drosophila, using in vivo two-photon calcium imaging of proprioceptors during controlled movements of the fly tibia. We found that the axons of leg proprioceptors are organized into distinct functional projections that contain topographic representations of specific kinematic features. Using subtype-specific genetic driver lines, we show that one group of axons encodes tibia position (flexion/extension), another encodes movement direction, and a third encodes bidirectional movement and vibration frequency. Thus, proprioceptive sensing of a single leg joint is mediated by multiple subtypes of specialized sensory neurons. This architecture may help to maximize information transmission, processing speed, and robustness, which are critical for feedback control of the limbs during locomotion.

neuroscience↗