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Lu, Y.-L.

Publications and source records attributed to Lu, Y.-L..

9 recordsLinked to original sources
bioRxiv2024

Field EPSPs of dentate gyrus granule cells studied by selective optogenetic activation of hilar mossy cells in hippocampal slices.

Glutamatergic dentate gyrus (DG) mossy cells (MCs) innervate the primary DG cell type, granule cells (GCs). Numerous MC synapses are on GC proximal dendrites in the inner molecular layer (IML). However, field recordings of the GC excitatory postsynaptic potential (fEPSPs) have not been used to study this pathway selectively. Here we describe methods to selectively activate MC axons in the IML using mice with Cre recombinase expressed in MCs. Slices were made after injecting adeno-associated virus (AAV) encoding channelrhodopsin (ChR2) in the DG. In these slices, we show that fEPSPs could be recorded reliably in the IML in response to optogenetic stimulation of MC axons. Furthermore, fEPSPs were widespread across the septotemporal axis. However, fEPSPs were relatively weak because they were small in amplitude and did not elicit a significant population spike in GCs. They also showed little paired pulse facilitation. We confirmed the extracellular findings with patch clamp recordings of GCs despite different recording chambers and other differences in methods. Together the results provide a simple method for studying MC activation of GCs and add to the evidence that this input is normally weak but widespread across the GC population. KEY POINTSO_LIWe describe a method to activate the MC input to GCs selectively using optogenetics in hippocampal slices C_LIO_LIMC excitation is weakly excitatory but so common among GCs that a field EPSP is generated at the site of MC synapses on GCs C_LIO_LIMC excitation of GCs is consistent across the septotemporal axis and contralaterally C_LIO_LIUsing the characteristics of optogenetically-evoked fEPSPs, electrical stimulation of the MC input to GCs can be optimized. C_LI

neuroscience↗
bioRxiv2023

Decision Characteristics Underlying Non-Suicidal Self-Injury in Patients with Major Depressive Disorder

BackgroundNon-suicidal self-injury (NSSI) behavior is significantly prevalent in both adolescents and psychiatric populations, particularly in individuals with major depressive disorder (MDD). NSSI can be considered a result of risky decision-making in response to negative emotions, where individuals choose self-harm over other less harmful alternatives, suggesting a potential decision-making deficit in those engaging in NSSI. This study delves into the complex relationship between NSSI and depression severity in decision-making and its cognitive underpinnings. MethodsWe assessed decision behaviors in 57 MDD patients with NSSI, 42 MDD patients without NSSI and 142 healthy controls using the Balloon Analogue Risk Task, which involves risk-taking, learning, and exploration in uncertain scenarios. Using computational modeling, we dissected the nuanced cognitive dimensions influencing decision behaviors. A novel statistical method was developed to elucidate the interaction effects between NSSI and depression severity. ResultsContrary to common perceptions, we found that individuals with NSSI behaviors were typically more risk-averse. Meanwhile, there was a complex interaction between NSSI and depression severity in shaping risk-taking behaviors. As depressive symptoms intensified, these individuals with NSSI began to perceive less risk and behave more randomly. ConclusionsThis research provides new insights into the cognitive aspects of NSSI and depression, highlighting the importance of considering the influence of comorbid mental disorders when investigating the cognitive underpinnings of such behaviors, especially in the context of prevalent cross-diagnostic phenomena like NSSI behaviors.

neuroscience↗
bioRxiv2023

Exploring the bounded rationality in human decision anomalies through an assemblable computational framework

Some seemingly irrational decision behaviors (anomalies), once seen as flaws in human cognition, have recently received explanations from a rational perspective. The basic idea is that the brain has limited cognitive resources to process the quantities (e.g., value, probability, time, etc.) required for decision making, with specific biases arising as byproducts of the resource allocation that is optimized for the environment. While appealing for providing normative accounts, the existing resource-rational models have limitations such as inconsistent assumptions across models, a focus on single environmental factors, and limited coverage of decision anomalies. One challenging anomaly is the peanuts effect, a pervasive phenomenon in decision-making under risk that implies an interdependence between the processing of value and probability. To extend the resource rationality approach to explain the peanuts effect, here we develop a computational framework--the Assemblable Resource-Rational Modules (ARRM)--that integrates ideas from different lines of boundedly-rational decision models as freely assembled modules. The framework can accommodate the joint functioning of multiple environmental factors, and allow new models to be built and tested along with the existing ones, potentially opening a wider range of decision phenomena to bounded rationality modeling. For one new and three published datasets that cover two different task paradigms and both the gain and loss domains, our boundedly-rational models reproduce two characteristic features of the peanuts effect and outperform previous models in fitting human decision behaviors.

neuroscience↗
bioRxiv2021

Methods for recording and imaging spreading depolarizations and seizure-like events in mouse hippocampal slices

Spreading depolarization (SD) is a sudden and synchronized depolarization of principal cells followed by depression of activity, which slowly propagates across brain regions like cortex or hippocampus. SD is considered to be mechanistically relevant to migraine, epilepsy, and traumatic brain injury. Interestingly, research into SD typically uses SD triggered immediately after a focal stimulus. Here we optimize an in vitro experimental model allowing us to record SD without focal stimulation. This method uses electrophysiological recordings and intrinsic optical imaging in slices. The method is also relatively easy and inexpensive. Acute hippocampal slices from mice or rats were prepared and used for extracellular and whole-cell recordings. Recordings were made in a submerged-style chamber with flow of artificial cerebrospinal fluid (aCSF) above and below the slices. Flow was fast (> 5ml/min), and temperature was 32{degrees}C. As soon as slices were placed in the chamber, aCSF containing 0 mM Mg2+ and 5 mM K+ (0 Mg2+/5 K+ aCSF) was used. Two major types of activity were observed: SD and seizure-like events (SLEs). Both occurred after many minutes of recording. Although both mouse and rat slices showed SLEs, only mouse slices developed SD and did so in the first hour of 0 Mg2+/5 K+ aCSF exposure. Intrinsic optical imaging showed that most SDs initiated in CA3 and could propagate into CA1 and dentate gyrus. In dentate gyrus, SD propagated in two separate waves: (1) into the hilus and (2) into granule cell and molecular layers simultaneously. This in vitro model can be used to better understand the mechanisms and relationship between SD and SLEs. It could also be useful in preclinical drug screening.

neuroscience↗
bioRxiv2021

Proteasome maturation factor UMP1 confers broad-spectrum disease resistance by modulating H2O2 accumulation in rice

Crops with broad-spectrum resistance (BSR) to diseases are highly desirable in agricultural production. Identification of BSR loci and dissection of the underlying mechanisms are fundamental for crop resistance breeding. Here, we describe the identification and characterization of a rice UMP1 allele, which confers race-nonspecific BSR against blast pathogen Magnaporthe oryzae. OsUMP1 encodes a proteasome maturation factor that contributes to 26S proteasome abundance and activity in rice. Modulation of OsUMP1 expression leads to proteome changes, particularly affects the amounts and activities of H2O2-degrading enzymes. Consequently, H2O2 accumulation and disease resistance are enhanced in OsUMP1-overexpressing rice but reduced in loss-of-function mutants. Elevation of OsUMP1 expression also promotes rice resistance to foliar pathogens Rhizoctonia solani and Xanthomonas oryzae pv. oryzae and a floral pathogen Ustilaginoidea virens without observable yield penalty. These results indicate a BSR pathway linking the proteasome machinery and H2O2 homeostasis, and provide a candidate gene for balancing BSR and yield traits in rice breeding. One Sentence SummaryA natural allele of rice UMP1 promotes resistance to multiple pathogens by boosting H2O2 accumulation.

plant biology↗
bioRxiv2020

Synergism between microRNA-124 and ELAVL3 drives neuronal gene upregulation during direct neuronal reprogramming of human fibroblasts

Neuron-enriched microRNAs (miRNAs), miR-9/9* and miR-124 (miR-9/9*-124), direct cell fate switching of human fibroblasts to neurons when ectopically expressed by repressing anti-neurogenic genes. How these miRNAs function after the onset of the transcriptome switch to a neuronal fate remains unclear. Here, we identified direct targets of miRNAs by Argonaute (AGO) HITS-CLIP as reprogramming cells activate the neuronal program and reveal the role of miR-124 that directly promotes the expression of its target genes associated with neuronal development and function. The mode of miR-124 as a positive regulator is determined by a neuron-enriched RNA-binding protein, ELAVL3, that interacts with AGO and binds target transcripts, whereas the non-neuronal ELAVL1 counterpart fails to elevate the miRNA-target gene expression. Although existing literature indicate that miRNA-ELAVL1 interaction can result in either target gene upregulation or downregulation in a context-dependent manner, we specifically identified neuronal ELAVL3 as the driver for miRNA target gene upregulation in neurons. In primary human neurons, repressing miR-124 and ELAVL3 led to the downregulation of genes involved in neuronal function and process outgrowth, and cellular phenotypes of reduced inward currents and neurite outgrowth. Results from our study support the role of miR-124 promoting neuronal function through positive regulation of its target genes.

neuroscience↗
bioRxiv2019

Data-Driven Design of Diagnostic Kits and Therapeutic Peptides

To ensure a physicochemically desired sequence motif to adapt a specific type of secondary structures, we compile an -helix database allowing complicate search patterns to facilitate a data-driven design of therapeutic peptides. Nearly 1.7 million helical peptides in >130 thousand proteins are extracted along with their interacting partners from the protein data bank (PDB). The sequences of the peptides are indexed with patterns and gaps and deposited in our Therapeutic Peptide Design dataBase (TP-DB). We here demonstrate its utility in three medicinal design cases. By our pattern-based search engine but not PHI-BLAST, we can identify a pathogenic protein, Helicobacter pylori neutrophil-activating protein (HP-NAP), a virulence factor of H. pylori, which contains a motif DYKYLE that belongs to the affinity determinant motif DYKXX[DE] of the FLAG-tag and can be recognized by the anti-FLAG M2 antibody. By doing so, the known purification-tag-specific antibody is repurposed into a diagnostic kit for H. pylori. Also by leveraging TP-DB, we discovered a stretch of helical peptide matching the potent membrane-insertion pattern WXXWXXW, elucidated by MD simulations. The newly synthesized peptide has a better minimal inhibitory concentration (MIC) and much lower cytotoxicity against Candida albicans (fungus) than that of previously characterized homologous antimicrobial peptides. In a similar vein, taking the discontinued anchoring residues in the helix-helix interaction interface as the search pattern, TP-DB returns several helical peptides as potential tumor suppressors of hepatocellular carcinoma (HCC) whose helicity and binding affinity were examined by MD simulations. Taken together, we believe that TP-DB and its pattern-based search engine provide a new opportunity for a (secondary-)structure-based design of peptide drugs and diagnostic kits for pathogens without inferring evolutionary homology between sequences sharing the same pattern. TP-DB is made available at http://dyn.life.nthu.edu.tw/design/.

bioinformatics↗
bioRxiv2018

Dlk1-Dio3 Locus-Derived LncRNAs Perpetuate Postmitotic Motor Neuron Cell Fate and Subtype Identity

The mammalian imprinted Dlk1-Dio3 locus produces multiple long non-coding RNAs (lncRNAs) from the maternally inherited allele, including Meg3 (i.e. Gtl2) in the mammalian genome. Although this locus has well-characterized functions in stem cell and tumor contexts, its role during neural development is unknown. By transcriptome profiling cell types at each stage of spinal cord development, we uncovered that lncRNAs expressed from the Dlk1-Dio3 locus are predominantly and gradually enriched in rostral motor neurons (MNs). Mechanistically, Meg3 and other Dlk1-Dio3 locus-derived lncRNAs facilitate Jarid2-Ezh2 interactions. Loss of these lncRNAs compromises the H3K27me3 landscape, leading to aberrant expression of progenitor and caudal Hox genes in postmitotic MNs. Our data illustrate that these lncRNAs in the Dlk1-Dio3 locus play a critical role in maintaining postmitotic MN cell fate by repressing progenitor genes and they shape MN subtype identity by regulating Hox genes, providing strong evidence of how lncRNAs function during embryonic development.

developmental biology↗