Biology subjects

Zhang, H.-Y.

Publications and source records attributed to Zhang, H.-Y..

10 recordsLinked to original sources

bioRxiv2026

PACAPergic BAC engages basolateral amygdalar and anterodorsal thalamic networks during looming-threat learning and memory in a labyrinth

The bed nucleus of the anterior commissure (BAC) is a small pituitary adenylate cyclase-activating polypeptide (PACAP)-rich glutamatergic cell population located at the intersection of the anterior commissure, stria terminalis, stria medullaris, and fornix. Here, we provide functional neuroanatomical characterization of the BAC using PACAP-Cre mice and Cre-dependent viral tracing. BAC axons traverse these major forebrain conduits to engage distributed limbic and diencephalic networks, with dense innervation of the posterior basolateral amygdala (pBLA) and anterior dorsal thalamic nucleus (AD), both implicated in emotional processing and spatial orientation. To determine the functional significance of the BAC, we developed a novel looming-threat memory test (LTMT) paradigm in which mice learned the location of a shelter within a dual-maze labyrinth before exposure to an overhead looming stimulus. Chemogenetic inhibition of BAC PACAP neurons impaired shelter-directed escape, increased freezing behavior, prolonged escape trajectories, and disrupted efficient safety-seeking responses. Selective deletion of PACAP from BAC neurons also blocked key aspects of the looming-induced behavioral phenotype. Fos mapping revealed robust neuronal activation by the looming stimulus, within the AD, pBLA, and dorsal periaqueductal gray (dPAG). BAC silencing blocked Fos induction. PACAPBAC depletion blocked fos induction in AD, but not in pBLA or dPAG. Preliminary ex-vivo recordings further indicated that PACAP modulates the intrinsic excitability of AD (and pBLA) neurons. Together, these findings identify the BAC as a previously unrecognized PACAPergic forebrain hub that links emotional and spatial-orientation networks to coordinate looming-threat learning, memory, and adaptive defensive behavior.

neuroscience↗

bioRxiv2025

Beyond Locomotion: How Specialized Motor Rhythms Enable Vertebrate Escape from Capture

Escape behaviors following capture are crucial for survival, yet their underlying neurobiological mechanisms remain poorly understood. We investigated how Xenopus laevis tadpoles use struggling movements to escape head restraint. High-speed video tracking revealed a stereotyped sequence of body flexions with distinct kinematics during capture and release. We further recorded motoneuron and motor nerve activity along the body axis during fictive struggling to reconstruct biologically realistic struggling commands, to drive the movement of a biomechanically detailed tadpole model. Simulations showed that struggling - characterized by long-duration, low-frequency, caudorostral muscle activation - was optimized to generate escape forces. Notably, hydrodynamic thrust alone proved insufficient for release. However, direct mechanical interactions between the tadpoles body and the restraining object generated additional reactive forces that facilitated escape. These findings demonstrate how animals use coordinated motor outputs and body mechanics to interact with environment to generate maximal freeing forces as the fundamental escape strategy.

neuroscience↗

bioRxiv2025

Targeted long-read RNA sequencing reveals the complexity of CLN3 transcription and the consequences of the most common 1-kb deletion in patients with juvenile CLN3 disease

Most genes are not yet fully annotated, and the extent of their transcript diversity and the roles and significance of specific isoforms is not understood. This information is therefore lacking for disease genes. The CLN3 gene underlies classic juvenile CLN3 disease, also known as juvenile neuronal ceroid lipofuscinosis, a rare paediatric neurodegenerative disorder. The most common cause of this biallelic disorder is a 1-kb intragenic deletion that removes two internal coding exons (exons 7 and 8). Here, we report findings from the first long-read RNA sequencing targeting CLN3 in blood samples derived from control individuals and from patients clinically and genetically diagnosed with juvenile CLN3 disease. We find that CLN3 transcription is complex, with >80 different transcripts encoding >35 different open reading frames (ORF) of different lengths, and no dominantly expressed transcript. The 1-kb deletion has direct consequences on this. This is consistent across patients, with total loss of some transcripts including those encoding the canonical 438 amino acid protein and other significant smaller isoforms. The highest expressed disease transcripts include those lacking exons 7 and 8 and encoding a 181 amino acid protein isoform, and other novel isoforms that lack additional exons and encode longer ORFs. The different effects on transcription of other CLN3 disease-causing variants are revealed in single patients. Together, these findings confirm the complexity of transcription at the CLN3 locus, reveal the impact of the 1-kb deletion and other variants on isoform abundance, and highlight the importance of understanding the contribution of these isoforms to CLN3 function in health and disease. Moreover, they impact the future design and development of personalised therapeutics and the design and generation of disease models. Finally, they underline the importance of full annotation for disease genes.

genetics↗

bioRxiv2025

Cocaine-induced immediate-early gene expression in the nucleus accumbens: roles of separate cAMP sensors

Immediate-early gene (IEG) induction after administration of amphetamine or cocaine has been used to trace the signaling pathways that mediate neuronal plasticity required for the short- and long-term behavioral effects of these psychostimulants. We recently reported that a novel cyclic AMP (cAMP)-dependent Rap guanine nucleotide exchange factor-2 (RapGEF2)-ERK signaling pathway is required for Egr-1 induction in D1 medium-spiny neurons (MSNs) of the nucleus accumbens (NAc) after cocaine treatment, and that its deletion from the NAc neurons attenuates cocaine-induced locomotor sensitization and conditioned place preference (CPP). However, the cell type-specific neuronal mechanisms underlying this effect remain unclear. In this study, we used Cre-LoxP technology and a novel Cre-amplifier transgene to generate conditional RapGEF2 knockout mice targeting D1-MSNs and investigated the functional role of RapGEF2 in cocaine reward. Deletion of RapGEF2 in D1-MSNs blocked cocaine-induced ERK phosphorylation (p-ERK) and Egr-1 induction. D1-MSN-specific RapGEF2 deletion did not affect intravenous cocaine self-administration, nor did it affect Fos induction by cocaine, prompting us to examine more closely the role of metabotropic (cAMP-dependent) signaling to IEGs after cocaine administration. We used a battery of D1-MSN-specific genetic interventions targeting cAMP signaling, including Drd1-Cre::Rap1A/Bfl/fl mice, and AAV injection of a Cre-dependent catalytically active phosphodiesterase (PDE4D3-cat) or a Cre-dependent protein kinase A-inhibitor (PKI) in the NAc of Drd1-Cre mice, to explore further the underlying cAMP dependence of IEG induction by acute and chronic cocaine administration, and the cAMP sensors required. Rap1 is reported as a necessary component for both RapGEF2- and PKA-dependent ERK activation, but a requirement for Rap in Fos induction by cocaine has not been examined. Deletion of Rap1A/B in D1-MSNs blocked cocaine-induced p-ERK and Egr-1 expression, but not c-Fos, supporting the idea that the RapGEF2-Rap1-ERK pathway specifically regulates Egr-1, not c-Fos, expression. D1-specific expression of the PDE4D3-cat ablated up-regulation of both Egr-1 and Fos in NAc after cocaine administration, demonstrating that induction of both IEGs requires cAMP elevation in D1-MSNs. Notably, inhibition of PKA activity via AAV-mediated expression of PKI-alpha in D1-MSNs blocked both c-Fos and Egr-1 induction. Thus, acute or chronic cocaine administration activates at least two cAMP-dependent signaling pathways in D1-MSNs: a PKA-Fos pathway and a RapGEF2-ERK-Egr-1 pathway. The finding that PKA also activates the ERK-Egr-1 signaling pathway by convergence on Rap1, and concomitantly activates c-Fos independently of Rap1, may underlie selective effects of metabotropic activation of RapGEF2 and PKA activation by cAMP on cocaine-dependent behaviors in mice.

neuroscience↗

bioRxiv2023

The P2 protein of wheat yellow mosaic virus acts as a VSR to facilitate virus infection in wheat plants

Wheat yellow mosaic virus (WYMV) causes severe viral wheat disease in Asia. The WYMV P1 protein encoded by RNA2 has viral suppressor of RNA silencing (VSR) activity to facilitate virus infection; however, VSR activity has not been identified for P2 protein encoded by RNA2. In this study, P2 protein exhibited strong VSR activity in Nicotiana benthamiana at the four-leaf stage, and point mutants P70A and G230A lost VSR activity. Protein P2 interacted with calmodulin (CaM) protein, a gene-silencing associated protein, while point mutants P70A and G230A did not interact with it. Competitive bimolecular fluorescence complementation and competitive co-immunoprecipitation experiments showed that P2 interfered with the interaction between CaM and calmodulin-binding transcription activator 3 (CAMTA3), but the point mutants P70A and G230A could not. Mechanical inoculation of wheat with in vitro transcripts of WYMV infectious cDNA clone further confirmed that VSR-deficient mutants P70A and G230A decreased WYMV infection in wheat plants compared with the wild type. In addition, RNA silencing, temperature, and autophagy had significant effects on accumulation of P2 protein in N. benthamiana leaves. In conclusion, WYMV P2 plays a VSR role in wheat and promotes virus infection by interfering with calmodulin-related antiviral RNAi defense. One-sentence summaryWYMV P2 protein exerts VSR activity by interfering with the CaM-CAMTA3 interaction to facilitate virus efficient systemic infection in wheat plants.

plant biology↗

bioRxiv2023

CLN3 transcript complexity revealed by long-read RNA sequencing analysis

BackgroundBatten disease is a group of rare inherited neurodegenerative diseases. Juvenile CLN3 disease is the most prevalent type, and the most common mutation shared by most patients is the "1-kb" deletion which removes two internal coding exons (7 and 8) in CLN3. Previously, we identified two transcripts in patient fibroblasts homozygous for the "1-kb" deletion: the "major" and "minor" transcripts. To understand the full variety of disease transcripts and their role in disease pathogenesis, it is necessary to first investigate CLN3 transcription in "healthy" samples without juvenile CLN3 disease. MethodsWe leveraged PacBio long-read RNA sequencing datasets from ENCODE to investigate the full range of CLN3 transcripts across various tissues and cell types in human control samples. Then we sought to validate their existence using data from different sources. ResultsWe found that a readthrough gene affects the quantification and annotation of CLN3. After taking this into account, we detected over 100 novel CLN3 transcripts, with no dominantly expressed CLN3 transcript. The most abundant transcript has median usage of 42.9%. Surprisingly, the known disease-associated "major" transcripts are detected. Together, they have median usage of 1.51% across 22 samples. Furthermore, we identified 48 CLN3 ORFs, of which 26 are novel. The predominant ORF that encodes the canonical CLN3 protein isoform has median usage of 66.7%, meaning around one-third of CLN3 transcripts encode protein isoforms with different stretches of amino acids. The same ORFs could be found with alternative UTRs. Moreover, we were able to validate the translational potential of certain transcripts using public mass spectrometry data. ConclusionOverall, these findings provide valuable insights into the complexity of CLN3 transcription, highlighting the importance of studying both canonical and non-canonical CLN3 protein isoforms as well as the regulatory role of UTRs to fully comprehend the regulation and function(s) of CLN3. This knowledge is essential for investigating the impact of the "1-kb" deletion and rare mutations on CLN3 transcription and disease pathogenesis.

genetics↗

bioRxiv2021

The genome of an apodid holothuroid (Chiridota heheva) provides insights into its adaptation to deep-sea reducing environment

Cold seeps and hydrothermal vents are deep-sea reducing environments that are characterized by a lack of oxygen, photosynthesis-derived nutrients and a high concentration of reducing chemicals. Apodida is an order of deep-sea echinoderms lacking tube feet and complex respiratory trees, which are commonly found in holothurians. Chiridota heheva Pawson & Vance, 2004 (Apodida: Chiridotidae) is one of the few echinoderms that resides in deep-sea reducing environments. Unlike most cold seep and hydrothermal vent-dwelling animals, C. heheva does not survive by maintaining an epi- or endosymbiotic relationship with chemosynthetic microorganisms. The species acquires nutrients by extracting organic components from sediment detritus and suspended material. Here, we report a high-quality genome of C. heheva as a genomic reference for echinoderm adaptation to reducing environments. Chiridota heheva likely colonized its current habitats in the early Miocene. The expansion of the aerolysin-like protein family in C. heheva compared with other echinoderms might be involved in the disintegration of microbes during digestion, which in turn facilitates the species adaptation to cold seep environments. Moreover, several hypoxia-related genes were subject to positive selection in the genome of C. heheva, which contributes to their adaptation to hypoxic environments.

genomics↗

bioRxiv2020

Interpreting the dynamic pathogenesis of Parkinson's disease by longitudinal blood transcriptome analysis

Achieving an improved understanding of the temporal sequence of factors involved in Parkinsons disease (PD) pathogenesis may accelerate drug discovery. In this study, we performed a longitudinal transcriptome analysis to identify associated genes underlying the pathogenesis of PD at three temporal phases. We firstly found that multiple initiator genes, which are related to processes of olfactory transduction and stem cell pluripotency, indicate PD risk to those subjects at the prodromal phase. And many facilitator genes involved in calcium signaling and stem cell pluripotency contribute to PD onset. We next identified 325 aggravator genes whose expression could lead to disease progression through damage to dopaminergic synapses and ferroptosis via an integrative analysis with DNA methylation. Last, we made a systematic comparison of gene expression patterns across PD development and accordingly provided candidate drugs at different phases in an attempt to prevent the neurodegeneration process.

bioinformatics↗

bioRxiv2018

pyMeSHSim: an integrative python package to realize biomedical named entity recognition, normalization and comparison

SummaryComputing semantic similarity between two texts, like disease descriptions, has become important for many biomedical text mining applications. Here, we present PyMeSHSim, which is an integrative, lightweight and data-rich MeSH toolkit that recognizes biomedical named entities (bio-NEs) from texts, maps the bio-NEs to the controlled vocabulary MeSH and measures the semantic similarity between the MeSH terms.\n\nAvailabilityPackages source code and test datasets are available under the GPLv3 license at https://github.com/luozhhub/pyMeSHSim\n\nContactzhen-xia.chen@mail.hzau.edu.cn or zhy630@mail.hzau.edu.cn

bioinformatics↗

bioRxiv2017

High-frequency off-target mutagenesis induced by CRISPR/Cas9 in Arabidopsis and its prevention by improving specificity of the tools

Specificity of CRISPR/Cas9 tools has been a major concern along with the reports of their successful applications. We report unexpected observations of high frequency off-target mutagenesis induced by CRISPR/Cas9 in T1 Arabidopsis mutants although the sgRNA was predicted to have a high specificity score. We also present evidence that the off-target effects were further exacerbated in the T2 progeny. To prevent the off-target effects, we tested and optimized two strategies in Arabidopsis, including introduction of a mCherry cassette for a simple and reliable isolation of Cas9-free mutants and the use of highly specific mutant SpCas9 variants. Optimization of the mCherry vectors and subsequent validation found that fusion of tRNA with the mutant rather than the original sgRNA scaffold significantly improves editing efficiency. We then examined the editing efficiency of eight high-specificity SpCas9 variants in combination with the improved tRNA-sgRNA fusion strategy. Our results suggest that highly specific SpCas9 variants require a higher level of expression than their wild-type counterpart to maintain high editing efficiency. Additionally, we demonstrate that T-DNA can be inserted into the cleavage sites of CRISPR/Cas9 targets with high frequency. Altogether, our results suggest that in plants, continuous attention should be paid to off-target effects induced by CRISPR/Cas9 in current and subsequent generations, and that the tools optimized in this report will be useful in improving genome editing efficiency and specificity in plants and other organisms.

molecular biology↗