Biology subjects

Yu, J. Y.

Publications and source records attributed to Yu, J. Y..

7 recordsLinked to original sources

bioRxiv2024

Optimizing real-time phase detection in diverse rhythmic biological signals for phase-specificneuromodulation

AbstractClosed-loop, phase-specific neurostimulation is a powerful method to modulate ongoing brain activity for clinical and research applications. Phase-specific stimulation relies on estimating the phase of an ongoing oscillation in real time and issuing a control command at a target phase. Phase detection algorithms based on Fast Fourier transform (FFT) are widely used due to their computational efficiency and robustness. However, it is unclear how algorithm performance depends on the spectral properties of the input signal and how algorithm parameters can be optimized. We used offline simulation to evaluate the performance of three algorithms (endpoint-corrected Hilbert Transform, Hilbert Transform and phase mapping) on three rhythmic biological signals with distinct spectral properties (rodent hippocampal theta potential, human EEG alpha and human essential tremor). First, we found that algorithm performance was more strongly influenced by signal amplitude and frequency variation compared with signal to noise ratio. Second, our simulations showed that the size of the data window for phase estimation was critical for the performance of FFT-based algorithms, where the optimal data window corresponds to the period of the oscillation. We validated this prediction with real time phase detection of hippocampal theta oscillations in freely behaving rats performing spatial navigation. Our findings define the relationship between signal properties and algorithm performance and provide a convenient method for optimizing FFT-based phase detection algorithms.

neuroscience↗

bioRxiv2024

Rectal Swab DNA Collection Protocol for PCR Genotyping in Rats

DNA collection is essential for genotyping laboratory animals. However, common collection methods require tissue amputation, causing discomfort and injury. Rectal swabbing has been proposed as an effective non-invasive alternative, but an evidence-backed protocol for the technique remains unavailable. We evaluate the effect of collection parameters on PCR result quality and present a genotyping protocol that can yield results for a litter of rats within 3-5 hours. We found that samples with 2-8 scrapes produced enough DNA to amplify targets up to [~]1800bp long using PCR. Rectal swabbing produced PCR results with similar quality to ear clip samples, and results were unaffected by residual fecal matter or cell debris. Our protocol enables fast, non-invasive, and repeatable genotyping using commercial PCR reagents.

molecular biology↗

bioRxiv2023

Experience shapes initial exploration for non-generalizable spatial learning

Experience can change how individuals learn. Learning to solve a new problem can be accelerated by generalizing known rules in the new context, but the impact of experience on solving problems where generalization cannot be applied remains unclear. To study the impact of experience on solving new problems that are distinct from previously learned tasks, we examined how rats learned a new spatial navigation task after having previously learned different sets of spatial navigation tasks. The new task differed from the previous tasks in spatial layout and navigation rule, and could not be solved by applying previously learned rules. We found that different experience histories did not impact task performance in the new task. However, by examining navigation choices made by rats, we found exploration patterns during the early stage of learning in the new task was dependent on experience history. We identified these behavioral differences by analyzing each rats navigation choices and by modeling their choice sequences with a modified distance dependent Chinese restaurant process. We further pinpointed the behavioral difference to sequential turn/no turn decisions made at choice points. Our results indicate that experience can influence problem-solving strategies when learning to solve new problems. Individuals with distinct experience histories can approach new problems from different starting points but converge on the same solution.

neuroscience↗

bioRxiv2020

Prefrontal cortical activity predicts the extra-place field spiking of hippocampal place cells

The receptive field of a neuron describes the regions of a stimulus space where the neuron is consistently active. Sparse spiking outside of the receptive field is often considered to be noise, rather than a reflection of information processing. Whether this characterization is accurate remains unclear. We therefore contrasted the sparse, temporally isolated spiking of hippocampal CA1 place cells to the consistent, temporally adjacent spiking seen within their spatial receptive fields ("place fields"). We found that isolated spikes, which occur during locomotion, are more strongly phase coupled to hippocampal theta oscillations than adjacent spikes and, surprisingly, transiently express coherent representations of non-local spatial representations. Further, prefrontal cortical activity is coordinated with, and can predict the occurrence of future isolated spiking events. Rather than local noise within the hippocampus, sparse, isolated place cell spiking reflects a coordinated cortical-hippocampal process consistent with the generation of non-local scenario representations during active navigation.

neuroscience↗

bioRxiv2018

Knock-in rat lines with Cre recombinase at the dopamine D1 and adenosine 2a receptor loci.

Genetically-modified mice have become standard tools in neuroscience research. Our understanding of the basal ganglia in particular has been greatly assisted by BAC mutants with selective transgene expression in striatal neurons forming the direct or indirect pathways. However, for more sophisticated behavioral tasks and larger intracranial implants, rat models are preferred. Furthermore, BAC lines can show variable expression patterns depending upon genomic insertion site. We therefore used CRISPR/Cas9 to generate two novel knock-in rat lines specifically encoding Cre recombinase immediately after the dopamine D1 receptor (Drd1a) or adenosine 2a receptor (Adora2a) loci. Here we validate these lines using in situ hybridization and viral vector mediated transfection to demonstrate selective, functional Cre expression in the striatal direct and indirect pathways respectively. We used whole-genome sequencing to confirm the lack of off-target effects, and established that both rat lines have normal locomotor activity and learning in simple instrumental and Pavlovian tasks. We expect these new D1-Cre and A2a-Cre rat lines will be widely used to study both normal brain functions and neurological and psychiatric pathophysiology.

neuroscience↗

bioRxiv2018

Knock-in rats expressing Cre and Flp recombinases at the Parvalbumin locus.

Rats have the ability to learn and perform sophisticated behavioral tasks, making them very useful for investigating neural circuit functions. In contrast to the extensive mouse genetic toolkit, the paucity of recombinase-expressing rat models has limited the ability to monitor and manipulate molecularly-defined neural populations in this species. Here we report the generation and validation of two knock-in rat strains expressing either Cre or Flp recombinase under the control of Parvalbumin (Pvalb), a gene expressed in the critical \"fast-spiking\" subset of inhibitory interneurons (FSIs). These strains were generated with CRISPR-Cas9 gene editing and show highly specific and penetrant labeling of Pvalb-expressing neurons, as demonstrated by in situ hybridization and immunohistochemistry. We validated these models in both prefrontal cortex and striatum using both ex vivo and in vivo approaches, including whole-cell recording, optogenetics, extracellular physiology and photometry. Our results demonstrate the utility of these new transgenic models for a wide range of neuroscience experiments.

neuroscience↗

bioRxiv2017

Specific hippocampal representations are linked to generalized cortical representations in memory.

Memories link information about specific experiences to more general knowledge that is abstracted from and contextualizes those experiences, but how neuronal activity patterns support this link is not known. Here we show that during memory reactivation in a foraging task with multiple spatial paths, specific hippocampal place representations are concurrently and preferentially reactivated with a subset of prefrontal cortical task representations that generalize across different paths. This link between specific and general representations may serve as a neural substrate for abstraction and task guidance in mammals.

neuroscience↗