Biology subjects

Sasaki, Y.

Publications and source records attributed to Sasaki, Y..

47 records · Page 3Linked to original sources

bioRxiv2020

Genome-scale metabolic rewiring to achieve predictable titers rates and yield of a non-native product at scale

Achieving high titer rates and yields (TRY) remains a bottleneck in the production of heterologous products through microbial systems, requiring elaborate engineering and many iterations. Reliable scaling of engineered strains is also rarely addressed in the first designs of the engineered strains. Both high TRY and scale are challenging metrics to achieve due to the inherent trade-off between cellular use of carbon towards growth vs. target metabolite production. We hypothesized that being able to strongly couple product formation with growth may lead to improvements across both metrics. In this study, we use elementary mode analysis to predict metabolic reactions that could be targeted to couple the production of indigoidine, a sustainable pigment, with the growth of the chosen host, Pseudomonas putida KT2440. We then filtered the set of 16 predicted reactions using -omics data. We implemented a total of 14 gene knockdowns using a CRISPRi method optimized for P. putida and show that the resulting engineered P. putida strain could achieve high TRY. The engineered pairing of product formation with carbon use also shifted production from stationary to exponential phase and the high TRY phenotype was maintained across scale. In one design cycle, we constructed an engineered P. putida strain that demonstrates close to 50% maximum theoretical yield (0.33 g indigoidine/g glucose consumed), reaching 25.6 g/L indigoidine and a rate of 0.22g/l/h in exponential phase. These desirable phenotypes were maintained from batch to fed-batch cultivation mode, and from 100ml shake flasks to 250 mL ambr(R) and 2 L bioreactors.

bioengineering↗

bioRxiv2019

Reward evokes visual perceptual learning following reinforcement rules

Visual perceptual learning (VPL) is defined as a long-term performance enhancement as a result of visual experiences. A number of studies have demonstrated that reward can evoke VPL. However, the mechanisms of how reward evoke VPL remain unknown. One possible hypothesis is that VPL is obtained through reward related reinforcement processing. If this hypothesis is true, learning can only occur when reward follows the stimulus presentation. Another interpretation is that VPL is acquired through an enhancement of alertness in association with reward. If the alertness hypothesis is true, learning should occur when reward precedes the stimulus presentation. In our study, we tested the plausibility of the two hypotheses by manipulating the order of reward and stimulus presentation. In Experiment 1, we separated participants into two groups. During training, the Before group received water reward 400ms prior to the onset of trained orientation stimulus while the After group received water reward 400ms subsequent to the onset of trained orientation stimulus. Both groups were trained using the Continuous Flash Suppression paradigm to render the stimulus imperceptible to the participants by the presentation of dynamic noise in the untrained eye. We found training only in the After group indicating that reward may evoke learning through reinforcement-like processing. In Experiment 2, we excluded the possibility that alertness may not be sufficient to elicit learning when presented before stimulus. We presented beep sound prior to the onset of stimulus to increase alertness. Our finding demonstrated that alertness is sufficient enough to evoke learning. In conclusion, our study provided evidence that reward can evoke VPL through reinforcement process.

neuroscience↗

bioRxiv2019

The \"Locus of Learning\" Problem: Effects of Stimulus and Task Structure on Temporal Perceptual Learning

The ability to discriminate sub-second intervals can be improved with practice, a process known as temporal perceptual learning (TPL). A central question in TPL is whether training improves the low-level sensory representation of a temporal interval or optimizes a set of task-specific response strategies. Here, we trained three groups of participants over five days on a single-interval temporal discrimination task using either fixed intervals (FI) or random intervals (RI). Before and after training, discrimination thresholds were also obtained on an untrained task. Our results revealed that only the FI group showed improvements with five days of training, but this learning did not generalize from the trained task to the untrained task in any group. These results highlight task-specificity in TPL and suggest that training-dependent improvements in timing ability might reflect an active reweighting of decision units, in addition to refinements in the sensory representation of a learned interval.

neuroscience↗

bioRxiv2019

Perceptual learning of lesions in mammograms induced by response feedback during training

Detecting subtle lesions in mammograms indicative of early breast cancer usually requires years of experience. Well-designed training paradigms could be a strong tool for promoting perceptual learning (PL) with rapid and long-lasting improvement in detectability of these subtle mammographic lesions. Given that PL occurs without feedback about the accuracy of subjects responses, the role of feedback has been completely ignored in clinical applications of PL. However, in this study, we found that the contents of the feedback profoundly and differentially influence the formation and retention of PL to detect calcification and architectural distortion lesions, two types of mammographic lesions that are frequently missed in mammographic screenings. We trained subjects to detect one type of lesion in a mammogram and manipulated the content of the response feedback during training for 3 groups (no feedback, correctness only, and both correctness and location of the lesion). We found that PL occurred for both lesions when both correctness and location feedback were provided. PL also occurred for calcifications but not for distortions when only correctness was provided. No learning occurred without feedback for either lesion. A retest conducted six months later showed that PL was retained only in the group with both correctness and location feedback for both types of lesions. In contrast to the general consensus of basic PL studies, our results demonstrate that the content of the response feedback is a determining factor in forming and retaining PL to detect mammographic lesions.

neuroscience↗

bioRxiv2019

Opponent neurochemical and functional processing in NREM and REM sleep in visual learning

Sleep is beneficial for learning. However, whether NREM or REM sleep facilitates learning, whether the learning facilitation results from plasticity increases or stabilization and whether the facilitation results from learning-specific processing are all controversial. Here, after training on a visual task we measured the excitatory and inhibitory neurochemical (E/I) balance, an index of plasticity in human visual areas, for the first time, while subjects slept. Off-line performance gains of presleep learning were associated with the E/I balance increase during NREM sleep, which also occurred without presleep training. In contrast, increased stabilization was associated with decreased E/I balance during REM sleep only after presleep training. These indicate that the above-mentioned issues are not matters of controversy but reflect opposite neurochemical processing for different roles in learning during different sleep stages: NREM sleep increases plasticity leading to performance gains independently of learning, while REM sleep decreases plasticity to stabilize learning in a learning-specific manner.

neuroscience↗

bioRxiv2019

Reward does not facilitate visual perceptual learning until sleep occurs

A growing body of evidence indicates that visual perceptual learning (VPL) is enhanced by reward provided during training. Another line of studies has shown that sleep following training also plays a role in facilitating VPL, an effect known as the offline performance gain of VPL. However, whether the effects of reward and sleep interact on VPL remains unclear. Here, we show that reward interacts with sleep to facilitate offline performance gains of VPL. First, we demonstrated a significantly larger offline performance gain over a 12-h interval including sleep in a reward group than that in a No-reward group. However, the offline performance gains over the 12-h interval without sleep were not significantly different with or without reward during training, indicating a crucial interaction between reward and sleep in VPL. Next, we tested whether neural activations during posttraining sleep were modulated after reward was provided during training. Reward provided during training enhanced REM sleep time, increased oscillatory activities for reward processing in the prefrontal region during REM sleep, and inhibited neural activation in the untrained region in early visual areas in NREM and REM sleep. The offline performance gains were significantly correlated with oscillatory activities of visual processing during NREM sleep and reward processing during REM sleep in the reward group but not in the No-reward group. These results suggest that reward provided during training becomes effective during sleep, with excited reward processing sending inhibitory signals to suppress noise in visual processing, resulting in larger offline performance gains over sleep.\n\nSignificance statementIndependent lines of research have shown that visual perceptual learning (VPL) is improved by reward or sleep. Here, we show that reward provided during training increased offline performance gains of VPL over sleep. Moreover, during posttraining sleep, reward was associated with longer REM sleep, increased activity in reward processing in the prefrontal region during REM sleep, and decreased activity in the untrained region of early visual areas during NREM and REM sleep. Offline performance gains were correlated with modulated oscillatory activity in reward processing during REM sleep and visual processing during NREM sleep. These results suggest that reward provided during training becomes effective on VPL through the interaction between reward and visual processing during sleep after training.

neuroscience↗

bioRxiv2019

Night watch during REM sleep for the first-night effect

We experience disturbed sleep in a new place, and this effect is known as the first-night effect (FNE) in sleep research. We previously demonstrated that the FNE was associated with a protective night-watch system during NREM sleep in one hemisphere, which is shown as interhemispheric asymmetry in sleep depth in the default-mode network (DMN), and interhemispheric asymmetry in increased vigilance to monitor external stimuli. The present study investigated whether rapid eye movement (REM) sleep exhibited a form similar to a night-watch system during NREM sleep. First, we tested whether theta activity, which is an index of the depth of REM sleep, showed interhemispheric asymmetry in association with the FNE, by source-localizing to the DMN. However, interhemispheric asymmetry in theta activity during REM sleep was not found in association with the FNE. Next, we tested whether vigilance, as measured by evoked brain responses to deviant sounds, was increased in one hemisphere and showed interhemispheric asymmetry in association with the FNE during REM sleep. Because vigilance is different between the phasic period where rapid eye movements occur and the tonic period where rapid eye movements do not occur during REM sleep, REM sleep was split into phasic and tonic periods for measurements of evoked brain responses. While the evoked brain responses are generally small during the phasic period without the FNE, we found that the evoked brain response was significantly augmented by the FNE during the phasic period. In contrast, the evoked brain response during the tonic period did not differ by the presence of the FNE. Interhemispheric asymmetry in brain responses was not found during the phasic or tonic periods. These results suggest that a night-watch system for the FNE appears as interhemispheric asymmetry in sleep depth and vigilance during NREM sleep, but it appears as increased vigilance in both hemispheres during the phasic period, when vigilance to external stimuli is generally reduced without the FNE, during REM sleep. Therefore, a night-watch system associated with the FNE may be subserved by different neural mechanisms during NREM and REM sleep.

neuroscience↗

bioRxiv2019

Prior physical synchrony enhances rapport and inter-brain synchronization during subsequent educational communication

Physical synchrony has been suggested to have positive effects on not only concurrent but also subsequent communication, but the underlying neural processes are unclear. Using functional near-infrared spectroscopy (fNIRS) hyperscanning, we tested the effects of preceding physical synchrony on subsequent dyadic teaching-learning communication. Thirty-two pairs of participants performed two experimental sessions. In each session, they underwent a rhythmic arm movement block with synchronous or asynchronous conditions, and then taught/learned unknown words to/from each other according to a given scenario. Neural activities in their medial and left lateral prefrontal cortex (PFC) were measured and inter-brain synchronization (IBS) during the teaching-learning blocks was evaluated. Participants rated their subjective rapport during the teaching-learning blocks, and took a word memory test. The analyses revealed that (1) prior physical synchrony enhanced teacher-learner rapport; (2) prior physical synchrony also enhanced IBS in the lateral PFC; and (3) IBS changes correlated positively with rapport changes. Physical synchrony did however not affect word memory performance. These results suggest that IBS can be useful to measure the effects of social-bonding facilitation activities for educational communication.

neuroscience↗

bioRxiv2018

Causal evidence for LTP-based interference in visual learning

Training related skills in close succession results in interference but the reasons for this interference are not understood. Here we test the hypothesis that interference occurs due to competition of long-term potentiation (LTP): the LTP induced by one task impedes the LTP induced by the other. Human subjects performed two consecutive training sessions on different Gabor orientations. Immediately after the offset of the first training, we applied continuous theta burst stimulation (cTBS) to interfere with the LTP processes produced by the first training. We found that cTBS to a control site (vertex) resulted in substantial anterograde interference for the second training. Critically, cTBS to the visual cortex not only disrupted learning on the immediately preceding training, but also released the second training from the anterograde interference. These results provide strong support for the LTP-based theory of interference and suggest the possibility of directly manipulating the competition between different learning periods.

neuroscience↗

bioRxiv2018

Trained-feature specific offline learning in an orientation detection task

It has been suggested that sleep provides additional enhancement of visual perceptual learning (VPL) acquired before sleep, termed offline performance gains. A majority of the studies that found offline performance gains of VPL used discrimination tasks including the texture discrimination task (TDT). This makes it questionable whether offline performance gains on VPL are generalized to other visual tasks. The present study examined whether a Gabor orientation detection task, which is a standard task in VPL, shows offline performance gains. In Experiment 1, we investigated whether sleep leads to offline performance gains on the task. Subjects were trained with the Gabor orientation detection task, and re-tested it after a 12-hr interval that included either nightly sleep or only wakefulness. We found that performance on the task improved to a significantly greater degree after the interval that included sleep and wakefulness than the interval including wakefulness alone. In addition, offline performance gains were specific to the trained orientation. In Experiment 2, we tested whether offline performance gains occur by a nap. Also, we tested whether spontaneous sigma activity in early visual areas during non-rapid eye movement (NREM) sleep, previously implicated in offline performance gains of TDT, was associated with offline performance gains of the task. A different group of subjects had a nap with polysomnography. The subjects were trained with the task before the nap and re-tested after the nap. The performance of the task improved significantly after the nap only on the trained orientation. Sigma activity in the trained region of early visual areas during NREM sleep was significantly larger than in the untrained region, in correlation with offline performance gains. These aspects were also found with VPL of TDT. The results of the present study demonstrate that offline performance gains are not specific to a discrimination task such as TDT, and can be generalized to other forms of VPL tasks, along with trained-feature specificity. Moreover, the present results also suggest that sigma activity in the trained region of early visual areas plays an important role in offline performance gains of VPL of detection as well as discrimination tasks.

neuroscience↗

bioRxiv2017

Feature-specific awake reactivation in human V1 after visual training

Converging human studies have demonstrated that brain activity patterns observed during task performance reemerge in the following restful awake state. Such \"awake reactivation\" has been demonstrated across higher-order cortex for complex images or associations. However, it remains unclear what specific training components are reactivated in these studies. Here we sought to provide evidence for the reactivation of a particular visual feature - Gabor orientation. Following extensive training on a visual task, we found robust reactivation in human V1 that lasted at least eight minutes. This effect was not present in higher retinotopic areas such as V2, V3, V3A, or V4v, demonstrating that the effects in V1 are not due to top-down processes such as conscious rehearsal. Furthermore, the amount of awake reactivation predicted the amount of performance improvement on the visual task. These results demonstrate that functionally-relevant awake reactivation of specific visual features occurs in early sensory cortex.

neuroscience↗