Biology subjects

Yan, L.

Publications and source records attributed to Yan, L..

At least 55 records · Page 3Linked to original sources

bioRxiv2024

Distinct Binding Modes of Inter-Spike Cross-Linking Suggest a Supplementary Mechanism for SARS-CoV-2 Antibody Neutralization

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its Omicron subvariants drastically amplifies transmissibility, infectivity, and immune escape, mainly due to their resistance to most neutralizing antibodies. Thus, exploring the mechanisms underlying antibody evasion is crucial. Although the full-length native form of antibody, immunoglobulin G (IgG), offers valuable insights into the neutralization, structural investigations primarily focus on the fragment of antigen-binding (Fab). Here, we employ single-particle cryo-electron microscopy (cryo-EM) to characterize a W328-6H2 antibody, in its native IgG form complexed with severe acute respiratory syndrome (SARS), severe acute respiratory syndrome coronavirus 2 wild-type (WT) and Omicron variant BA.1 spike protein (S). Three high-resolution structures reveal that the full-length IgG forms a centered head-to-head dimer of trimer when bound fully stoichiometrically with both SARS and WT S, while adopting a distinct offset configuration with Omicron BA.1 S. Combined with functional assays, our results suggest that, beyond the binding affinity between the RBD epitope and Fab, the higher-order architectures of S trimer and full-length IgG play an additional role in neutralization, elucidate a potential molecular basis of Omicron immune escape, and expand our understanding on antibody evasion mechanisms.

immunology↗

bioRxiv2024

Therapeutic targeting of Syndecan-1 axis overcomes acquired resistance to KRAS-targeted therapy in gastrointestinal cancers

The therapeutic benefit of recently developed mutant KRAS (mKRAS) inhibitors has been limited by the rapid onset of resistance. Here, we aimed to delineate the mechanisms underlying acquired resistance to mKRAS inhibition and identify actionable targets for overcoming this clinical challenge. Previously, we identified Syndecan-1 (SDC1) as a key effector for pancreatic cancer progression whose surface expression is driven by mKRAS. By leveraging both pancreatic and colorectal cancer models, we found that surface SDC1 expression was initially diminished upon mKRAS inhibition, but recovered in tumor cells that bypass mKRAS dependency. Functional studies showed that these tumors depended on SDC1 for survival, further establishing SDC1 as a driver for the acquired resistance to mKRAS inhibition. Mechanistically, we revealed that the YAP1-SDC1 axis was the major driving force for bypassing mKRAS dependency to sustain nutrient salvage machinery and tumor maintenance. Specifically, YAP1 activation mediated the recovery of SDC1 localization on cell surface that sustained macropinocytosis and enhanced the activation of multiple RTKs, promoting resistance to KRAS-targeted therapy. Overall, our study has provided the rationale for targeting the YAP-SDC1 axis to overcome resistance to mKRAS inhibition, thereby revealing new therapeutic opportunities for improving the clinical outcome of patients with KRAS-mutated cancers.

cancer biology↗

bioRxiv2024

Ganoderma lucidum alleviates kidney aging by modulating gut microbiota

BackgroundGanoderma lucidum, a renowned traditional Chinese medicine known for its multiple health benefits, including anti-aging effect, has the ability to influence gut microbiota. However, its specific role in alleviating aging via gut microbiota has not been thoroughly investigated. Here, we explored the impact of G. lucidum sporoderm-broken spore powder (Gl-SBSP) on kidney aging using naturally aged and radiation-induced premature senescence mouse models. MethodsWe analyzed gut microbiota through high-throughput sequencing in naturally aged and radiation-induced premature senescence mice after oral administration of Gl-SBSP. Additionally, untargeted metabolomics of the gut microbiome in naturally aged mice was performed using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) analyses. Transcriptomics was employed to systematically measure gene expression levels throughout kidney tissues. ResultsGl-SBSP effectively mitigated aging-related phenotypic changes and significantly alleviated kidney aging, although outcomes were mixed in the irradiation mouse model. Importantly, Gl-SBSP modulated gut bacterial composition, particularly enriching Lachnospiraceae in naturally aged mice and in radiation-induced premature senescence mice with positive prognostic outcomes. Nicotinamide riboside (NR), derived from Lachnospiraceae bacteria, was identified as a potential metabolite that promoted recovery of senescent kidneys and improved renal function, validated through in vitro and in vivo experiments. Transcriptome analysis revealed that NR regulates kidney steroid metabolism in aging. ConclusionOur findings suggest that Gl-SBSPs anti-aging effect is mediated by NR derived from the Lachnospiraceae family, influencing kidney steroid metabolism via the gut-kidney axis. These results provide new insights into the mechanisms underlying the anti-aging properties of Gl-SBSP. AbstractGanoderma lucidum, also known as "Linzhi," is a well-established traditional Chinese medicine renowned for its multiple health benefits and its influence on gut microbiota. In this study, we investigated the anti-aging effect of G. lucidum sporoderm-broken spore powder (Gl-SBSP) through the gut-kidney axis using naturally aged and radiation-induced premature senescence mouse models. Administration of Gl-SBSP not only effectively mitigated aging-related phenotypic changes but also significantly alleviated kidney aging, although outcomes were mixed in the irradiation model. Importantly, Gl-SBSP modulated gut bacterial composition, particularly enriching Lachnospiraceae in naturally aged mice and in radiation-induced premature senescence mice with favorable and long-lasting outcomes. Nicotinamide riboside (NR), derived from Lachnospiraceae bacteria, was identified as a potential metabolite that facilitated the rejuvenation of senescent kidneys and improved renal function through both in vitro and in vivo experiments. Further investigation revealed that NR regulated steroid metabolic process in kidney. Our findings suggest that the anti-aging effect of Gl-SBSP is mediated by NR derived from the Lachnospiraceae bacteria, thereby influencing kidney steroid metabolism through the gut-kidney axis. This study provides novel insights into the anti-aging mechanisms of Ganoderma.

microbiology↗

bioRxiv2024

Cerebrospinal Fluid Dynamics: Uncovering Alternative Blood Vessel Clearance Mechanisms

The pathways that run along the olfactory nerves crossing the cribriform plate and connecting to lymphatic vessels in the nasal cavity, have been identified as a crucial route for cerebrospinal fluid (CSF) outflow. However, the presence of a CSF efflux pathway through blood vessels in this region has yet to be clarified. This study aimed to elucidate the anatomical connections between the subarachnoid space and the bloodstream at the nasal epithelium and the venous drainage routes of the nasal epithelium in mice. Our findings demonstrated that CSF tracers could be drained not only through lymphatic vessels in the nasal cavity and cervical lymph nodes (CLNs), but also through the blood vessels in this area that extend to its venous drainage routes, including the facial and jugular veins. Additionally, we showed that ligation of CLNs neither impeded the influx and efflux of CSF tracers nor exacerbated Alzheimers disease (AD)-related pathology in AD mice. Our work reveals a previously unrecognized pathway for CSF drainage through blood vessels within the nasal mucosa. These findings provide insight into the efficient removal of waste products, facilitating optimal functioning of neural tissue within the susceptible tissue of our brains.

neuroscience↗

bioRxiv2024

Megabarcoding reveals a tale of two very different dark taxa along the same elevational gradient

AbstractOur planet is entering the sixth mass extinction without detailed spatio-temporal distribution and abundance information for most insect species. Particularly lacking is this information for dark taxa although they contain most animal species. This problem can be addressed with high-throughput single specimen barcoding (megabarcoding), but it remain unknown to what extent one dark taxon can be used as a proxy for another because of similar biodiversity patterns. This is here tested and we show that two Diptera taxa (Phoridae, Mycetophilidae) have very different spatio-temporal distributions across the same elevational gradient. We applied COI megabarcoding to samples collected every 14 days over three seasons at six elevations (800 to 1,800 m) in a temperate forest ecosystem in Northern China (Baihua Mountain Reserve). Elevation, precipitation, and temperature were used as environmental variables to understand the data obtained for 17,179 specimens representing 492 mOTUs of Phoridae and 2,281 specimens of 148 mOTUs of Mycetophilidae. Congruent is that the alpha diversity for both taxa increased in the summer and there is evidence for a mid-domain effect and phylogenetic clustering in high elevations. However, the extent and pattern of seasonal variation differed considerably. Phorid communities exhibited shifts between spring, summer and autumn seasons, but surprisingly little difference between elevations. In contrast, mycetophilid communities were structured along the elevational gradient and dependent on precipitation. Our study highlights the urgent need for obtaining detailed spatio-temporal information for the most diverse dark taxa, but also illustrates that these data can be readily obtained with megabarcoding.

ecology↗

bioRxiv2024

ZNF574 is a Quality Control Factor For Defective Ribosome Biogenesis Intermediates

Eukaryotic ribosome assembly is an intricate process that involves four ribosomal RNAs, 80 ribosomal proteins, and over 200 biogenesis factors that take part in numerous interdependent steps. This complexity creates a large genetic space in which pathogenic mutations can occur. "Dead-end" ribosome intermediates that result from biogenesis errors are rapidly degraded, affirming the existence of quality control pathway(s) that monitor ribosome assembly. However, the factors that differentiate between on-path and dead-end intermediates are unknown. We engineered a system to perturb ribosome assembly in human cells and discovered that faulty ribosomes are degraded via the ubiquitin proteasome system. We identified ZNF574 as a key component of a novel quality control pathway, which we term the Ribosome Assembly Surveillance Pathway (RASP). Loss of ZNF574 results in the accumulation of faulty biogenesis intermediates that interfere with global ribosome production, further emphasizing the role of RASP in protein homeostasis and cellular health.

cell biology↗

bioRxiv2024

A high-continuity and annotated reference genome of allotetraploid Siberian wildrye (Elymus sibiricus L., Poaceae: Triticeae)

Elymus sibiricus L. (Siberian wildrye, Es), a species belonging to the wheat tribe, is extensively employed as forage and for the reclamation of degraded grasslands within the Qinghai-Tibet Plateau (QTP). This study provides a high-quality reference genome assembly for the allotetraploid Es, which is composed of 14 pseudomolecules with the total genome size of 6.57 Gb. Our finding suggest that large-scale bursts of retrotransposons are critical for the genome expansion of Es. We discovered a translocation event between the Es4H and Es6H chromosomes with a low frequency of combination. Phylogenetic analyses of 90 Es accessions and 25 diploid accessions representing proposed ancestors from various habitats revealed the existence of four distinct populations. We further provided support for the hypothesis that the QTP is the center of origin and genetic diversity for Es. Collectively, our study offers valuable insights into the evolution of Es, as well as providing genomic resources for genetic enhancement in the Elymus genus and wheat tribe.

genomics↗

bioRxiv2024

The C. elegans uv1 neuroendocrine cells provide direct mechanosensory feedback of vulval opening

Neuroendocrine cells react to physical, chemical, and synaptic signals originating from tissues and the nervous system, releasing hormones that regulate various body functions beyond the synapse. Neuroendocrine cells are often embedded in complex tissues making direct tests of their activation mechanisms and signaling effects difficult to study. In the nematode worm C. elegans, four uterine-vulval (uv1) neuroendocrine cells sit above the vulval canal next to the egg-laying circuit, releasing tyramine and neuropeptides that feedback to inhibit egg laying. We have previously shown uv1 cells are mechanically deformed during egg laying, driving uv1 Ca2+ transients. However, whether egg-laying circuit activity, vulval opening, and/or egg release triggered uv1 Ca2+ activity was unclear. Here we show uv1 responds directly to mechanical activation. Optogenetic vulval muscle stimulation triggers uv1 Ca2+ activity following muscle contraction even in sterile animals. Direct mechanical prodding with a glass probe placed against the worm cuticle triggers robust uv1 Ca2+ activity similar to that seen during egg laying. Direct mechanical activation of uv1 cells does not require other cells in the egg-laying circuit, synaptic or peptidergic neurotransmission, or TRPV and Piezo channels. EGL-19 L-type Ca2+ channels, but not P/Q/N-type or Ryanodine Receptor Ca2+ channels, promote uv1 Ca2+ activity following mechanical activation. L-type channels also facilitate the coordinated activation of uv1 cells across the vulva, suggesting mechanical stimulation of one uv1 cells cross-activates the other. Our findings show how neuroendocrine cells like uv1 report on the mechanics of tissue deformation and muscle contraction, facilitating feedback to local circuits to coordinate behavior. Significance StatementNeuroendocrine cells respond to diverse physical and chemical signals from the body, releasing hormones that control reproduction, gut motility, and fight or flight responses. Neuroendocrine cells are often found embedded in complex tissues, complicating studies of how they are activated. Using the genetic and experimental accessibility of C. elegans, we find the uv1 neuroendocrine cells of the egg-laying motor behavior circuit respond directly to mechanical stimulation and vulval opening. We show that L-type voltage-gated Ca2+ channels facilitate uv1 mechanical activation and also coordinate cell activation across the vulval opening. In contrast to other mechanically activated cells, uv1 activation does not require Piezo or TRPV channels. This work shows how neuroendocrine cells relay critical mechanosensory feedback to circuits that control reproduction.

neuroscience↗

bioRxiv2024

Modulation of photosystem II heterogeneity and stomatal functioning contribute to sustaining photochemistry and photoprotection in mangroves exposed to a cold wave

Cold waves restrict the distribution of mangroves. This study examined the contribution of PSII heterogeneity and stomatal functioning to sustaining photochemistry and photoprotection in mangroves during a cold wave. We exposed eight populations of Kandelia obovata (cold-tolerant) and, Bruguiera gymnorhiza (cold-susceptible) from different latitudes to 27/20{degrees}C (favorable) and 10/3{degrees}C (chilling; simulated cold wave) day and night temperatures. Multiple trait responses imply that cold waves affected K. obovata the least. Significant changes in chlorophyll fluorescence transients (photosystem II [PSII]) with a slight decrease in the redox status of P700 (photosystem I [PSI]) imply a greater impact of a cold wave on PSII. During the cold wave, photochemical efficiency of PSII, efficiency of the water-splitting complex, light absorptance, stomatal pore area, cyclic electron flow, nonphotochemical quenching, and number of active PSII and PSII QB reducing centers decreased, while light transmittance, night respiration, and inactive PSII QB nonreducing, PSII{beta}, and {gamma} centers increased in both species. The population of K. obovata from the coldest latitudinal site (Fujian, China) was least affected by cold wave due to local evolutionary adaptations. Modulation of PSII heterogeneity and stomatal functioning is important to sustaining photochemistry and photoprotection in mangroves to cope with cold waves. HighlightsPSII heterogeneity and stomatal functioning support mangroves to cope with cold waves. Local evolutionary adaptations promote the cold tolerance of mangrove populations.

plant biology↗

bioRxiv2024

The Genomes of Nematode-Trapping Fungi Provide Insights into the Origin and Diversification of Fungal Carnivorism

Nematode-trapping fungi (NTF), most of which belong to a monophyletic lineage in Ascomycota, cannibalize nematodes and other microscopic animals, raising questions regarding the types and mechanisms of genomic changes that enabled carnivorism and adaptation to the carbon-rich and nitrogen-poor environment created by the Permian-Triassic extinction event. Here, we conducted comparative genomic analyses of 21 NTF and 21 non-NTF to address these questions. Carnivorism-associated changes include expanded genes for nematode capture, infection, and consumption (e.g., adhesive proteins, CAP superfamily, eukaryotic aspartyl proteases, and serine-type peptidases). Although the link between secondary metabolite (SM) production and carnivorism remains unclear, we found that the numbers of SM gene clusters among NTF are significantly lower than those among non-NTF. Significantly expanded cellulose degradation gene families (GH5, GH7, AA9, and CBM1) and contracted genes for carbon-nitrogen hydrolases (enzymes that degrade organic nitrogen to ammonia) are likely associated with adaptation to the carbon-rich and nitrogen-poor environment. Through horizontal gene transfer events from bacteria, NTF acquired the Mur gene cluster (participating in synthesizing peptidoglycan of the bacterial cell wall) and Hyl (a virulence factor in animals). Disruption of MurE reduced NTFs ability to attract nematodes, supporting its role in carnivorism. This study provides new insights into how NTF evolved and diversified after the Permian-Triassic mass extinction event.

evolutionary biology↗

bioRxiv2024

LncRNA-Snhg3 Aggravates Hepatic Steatosis by Regulating PPARγ via SND1/H3K27me3

LncRNAs are involved in modulating the individual risk and the severity of progression in metabolic dysfunction-associated fatty liver disease (MASLD), but their precise roles remain largely unknown. This study aimed to investigate the role of lncRNA Snhg3 in the development and progression of MASLD, along with the underlying mechanisms. The result showed that Snhg3 was significantly downregulated in the liver of high-fat diet-induced obesity (DIO) mice. Notably, palmitic acid promoted the expression of Snhg3 and overexpression of Snhg3 increased lipid accumulation in primary hepatocytes. Furthermore, hepatocyte-specific Snhg3 deficiency decreased body and liver weight, alleviated hepatic steatosis and promoted hepatic fatty acid metabolism in DIO mice, whereas overexpression induced the opposite effect. Mechanistically, Snhg3 promoted the expression, stability and nuclear localization of SND1 protein via interacting with SND1, thereby inducing K63-linked ubiquitination modification of SND1. Moreover, Snhg3 decreased the H3K27me3 level and induced SND1-mediated chromatin loose remodeling, thus reducing H3K27me3 enrichment at the Ppar{gamma} promoter and enhancing Ppar{gamma} expression. The administration of PPAR{gamma} antagonist T0070907 improved Snhg3-aggravated hepatic steatosis. Our study revealed a new signaling pathway, Snhg3/SND1/H3K27me3/PPAR{gamma}, responsible for MASLD and indicates that lncRNA-mediated epigenetic modification has a crucial role in the pathology of MASLD.

molecular biology↗

bioRxiv2024

Granzyme B-based CAR T cells block metastasis by eliminating circulating tumor cells

Chimeric antigen receptor (CAR) T cells have limited efficacy against solid tumors due to the hostile microenvironment. Circulating tumor cells (CTCs) are essential to metastasis, which is the cause of most of cancer-related death. Here, we generated GrB-CAR T cells targeting membrane-bound HSP70 (mHSP70), a highly tumor-specific antigen detected in numerous cancers. GrB-CAR T cells exhibited potent cytotoxicity against a broad spectrum of cancer cell lines and stem-like cancer cells in vitro and effectively inhibited xenograft tumor growth in vivo. Importantly, GrB-CAR T cells markedly decreased the number of CTCs and, therefore, hindered cancer metastasis in spontaneous metastasis models with uncontrollable primary tumor growth, a scenario commonly encountered in clinical trials of CAR T therapies for solid tumors. Furthermore, despite the 100% homology between human and macaque HSP70 protein, the autotransplantation of macaque T cells expressing human GrB-CAR did not cause any obvious toxic effects. These results not only demonstrate GrB-CAR T cells as a safe and effective tactic with broad-spectrum anticancer activity, but also offer strong experimental evidence and proof-of-concept validation for CAR T cell-mediated metastasis inhibition by targeting CTCs.

immunology↗

bioRxiv2024

Septo-hypothalamic regulation of binge-like alcohol consumption by the nociceptin system.

High intensity alcohol drinking during binge episodes overwhelmingly contributes to the socioeconomic burden created by Alcohol Use Disorders (AUD). Novel interventions are needed to add to the current therapeutic toolkit and nociceptin receptor (NOP) antagonists have shown promise in reducing heavy drinking days in patients with an AUD. However, an endogenous locus of nociceptin peptide and discrete sites of NOP action underlying this effect remains understudied. Here we show that the lateral septum (LS), a region contributing to binge drinking, is enriched in neurons expressing mRNA coding for the nociceptin peptide (Pnoc). Pnoc-expressing neurons of the LS (LSPnoc) are tuned to stimuli associated with negative valence and display increased excitability during withdrawal from binge-like alcohol drinking. LSPnoc activation was found to have aversive qualities and also potentiates binge-like drinking behavior, suggesting a convergence of circuitry that promotes aversion and drives alcohol consumption. Viral mediated tracing and functional assessment of LSPnoc projection fields revealed GABAergic synapses locally within the LS, and downstream within the lateral hypothalamus (LH) and supramammillary nucleus (SuM). Genetic deletion of NOP from the LS attenuated binge-like alcohol intake in male mice while NOP deletion from the LH and SuM decrease alcohol intake in females. Together, these findings are the first to demonstrate an endogenous population of nociceptin-expressing neurons that contributes to alcohol consumption and identifies sex-dependent modulation of alcohol drinking by NOP.

neuroscience↗

bioRxiv2024

A self-adaptive and versatile tool for eliminating multiple undesirable variations from transcriptome

Accurate identification of true biological signals from diverse undesirable variations in large-scale transcriptomes is essential for downstream discoveries. Herein, we develop a universal deep neural network, called DeepAdapter, to eliminate various undesirable variations from transcriptomic data. The innovation of our approach lies in automatic learning of the corresponding denoising strategies to adapt to different situations. The data-driven strategies are flexible and highly attuned to the transcriptomic data that requires denoising, yielding significant improvement in reducing undesirable variation originating from batches, sequencing platforms, and bio-samples with varied purity beyond manually designed schemes. Comprehensive evaluations across multiple batches, different RNA measurement technologies and heterogeneous bio-samples demonstrate that DeepAdapter can robustly correct diverse undesirable variations and accurately preserve biological signals. Our findings indicate that DeepAdapter can act as a versatile tool for the comprehensive denoising of the large and heterogeneous transcriptome across a wide variety of application scenarios.

bioinformatics↗

bioRxiv2023

ConBoTNet: supervised contrastive learning enhances MHC-II peptide binding affinity prediction

Accurate prediction of major histocompatibility complex (MHC)-peptide binding affinity can improve our understanding of cellular immune responses and guide personalized immunotherapies. Nevertheless, the existing deep learning-based approaches for predicting MHC-II peptide interactions fall short of satisfactory performance and offer restricted model interpretability. In this study, we propose a novel deep neural network, termed ConBoTNet, to address the above issues by introducing the designed supervised contrastive learning and bottleneck transformer extractors. Specifically, the supervised contrastive learning pre-training enhances the models representative and generalizable capabilities on MHC-II peptides by pulling positive pairs closer and pushing negative pairs further in the feature space, while the bottleneck transformer module focuses on MHC-II peptide interactions to precisely identify binding cores and anchor positions in an unsupervised manner. Extensive experiments on benchmark datasets under 5-fold cross-validation, leave-one-molecule-out validation, independent testing, and binding core prediction settings highlighted the superiority of our proposed ConBoTNet over current state-of-the-art methods. Data distribution analysis in the latent feature space demonstrated that supervised contrastive learning can aggregate MHC-II-peptide samples with similar affinity labels and learn common features of similar affinity. Additionally, we interpreted the trained neural network by associating the attention weights with peptides and innovatively find both well-established and potential peptide motifs. This work not only introduces an innovative tool for accurately predicting MHC-II peptide affinity, but also provides new insights into a new paradigm for modeling essential biological interactions, advancing data-driven discovery in biomedicine.

bioinformatics↗

bioRxiv2023

Olfaction foraging in visually oriented tropical arboreal ants Oecophylla smaragdina: Implications for insect predation studies using artificial sentinel prey

Predation is the key to understanding trophic interactions. Because of the brief and cryptic nature of predatory behavior, sentinel prey has been widely adopted as an indirect way to identify predators and understand trophic interactions. However, sentinel prey presents only static visual cues, potentially biasing toward visually oriented predators whilst ignoring those that require other sensory cues to forage. Despite this, the effectiveness of sentinel prey has rarely been tested. Here, we focused on the weaver ant, Oecophylla smaragdina, a keystone predator widespread in the Asian and Australian tropics. As this species has large eyes and is known to visually navigate in their arboreal habitats, we hypothesized that they rely on visual cues to forage and that their predatory behavior will be captured by caterpillar-shaped sentinel prey. Ants were collected as colonies, and preference trials on baits were conducted using combinations of olfactory and static visual cues including the caterpillar shape. Surprisingly, O. smaragdina showed little or no preference for baits in the absence of olfactory cues and did not differentiate the shapes of baits regardless of the presence of olfactory cues. Our results indicate that O. smaragdina is likely to make predatory decisions based primarily on olfactory cues, while visual cues might be used for other behaviors. Furthermore, O. smaragdina is likely to be left out by the predation studies using sentinel prey models which is particularly alarming considering the dominant role of this species in the trophic interactions of tropical rainforests. Our study demonstrates that morphological characteristics, arboreal habitats, and visually oriented behavior do not necessarily suggest the use of static visual cues for predatory decisions. We suggest that sentinel prey models should not be used alone when the dominant predators are unlikely to use visual cues to make predatory decisions.

ecology↗

bioRxiv2023

The SNARC effect involves both representation and response-selection processing stages: Evidence from ERPs

The processing stage (i.e., the early semantic representation stage, the late response-selection stage, or both) at which the spatial-numerical association of response codes (SNARC) effect occurs is still controversial. The two-stage processing model hypothesizes that the SNARC effect involves both stages and that different interference factors acting at the two stages might be the core reason for the observed stage flexibility of the SNARC effect. To test this hypothesis, the present study was designed to elicit the SNARC, Stroop (semantic-representation stage related), and Simon (response-selection stage related) effects together in one magnitude comparison task and used the event-related potentials (ERPs) to observe the temporal dynamics of these effects. The behavioral results showed no interaction between the Stroop and Simon effects, while these two effects both interacted with the SNARC effect. Furthermore, the ERP results showed an interaction of the Stroop effect with the SNARC effect for the early sensory P1 component, while the interaction of the Simon effect with the SNARC effect was evident for the late N2 and P300 components. The current study repeatedly verified the independence of Stroop and Simon effects. Most importantly, the temporal-specific interactions among the SNARC effect and the other two stage-related factors provided further evidence to support the two-stage processing model that the SNARC effect involves both the representation and response-selection stages.

neuroscience↗

bioRxiv2023

Brief change in dopamine activity during consolidation impairs long-term memory via sleep disruption

Sleep disturbances are associated with poor long-term memory (LTM) formation, yet the underlying cell types and neural circuits involved have not been fully decoded. Dopamine neurons (DANs) are involved in memory processing at multiple stages. Here, using both male and female flies, Drosophila melanogaster, we show that, during the first few hours of memory consolidation, disruption of basal activity of a small subset of protocerebral anterior medial DANs (PAM-DANs), by either brief activation or inhibition of the two dorsal posterior medial (DPM) neurons, impairs 24 h LTM. Interestingly, these brief changes in activity using female flies result in sleep loss and fragmentation, especially at night. Importantly, pharmacological rescue of sleep after manipulation restores LTM. A specific subset of PAM-DANs (PAM-1) that synapse onto DPM neurons specify the microcircuit that links sleep and memory. MBON-1 also contributes to the integration of sleep and memory by acting as an additional parallel circuit. PAM-DANs, including PAM-1, form functional synapses onto DPM mainly via two dopamine receptor subtypes. Dop1R1 primarily mediates the link between sleep and memory. This PAM-1 to DPM microcircuit exhibits a synchronized, transient, post-training change in activity during the critical memory consolidation window, suggesting an effect of this microcircuit on maintaining the sleep necessary for LTM consolidation. Our results provide a new molecular and circuit basis for the complex relationship between sleep and memory.

neuroscience↗