Biology subjects

Jin, M.

Publications and source records attributed to Jin, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Altered striatal dopamine regulation in ADGRL3 knockout mice

Dopaminergic signaling is essential for regulating movement, learning, and reward. Disruptions in this system are linked to neuropsychiatric disorders such as ADHD. ADGRL3, an adhesion G protein-coupled receptor highly expressed in the brain, is genetically associated with increased ADHD risk. ADGRL3 knockout in animals alters expression of dopaminergic markers and induces dopamine-related behavioral changes. However, its precise role in modulating dopamine signaling remains unclear. We investigated how ADGRL3 knockout affects striatal dopamine release in mice using ex vivo fast-scan cyclic voltammetry and in vivo fiber photometry with a dopamine sensor. Ex vivo measurements showed increased electrically-evoked dopamine release across the striatum. Conversely, in vivo recordings revealed reduced task-induced dopamine signals in the nucleus accumbens during an operant fixed interval task. This reduction was not due to impaired dopamine availability, as amphetamine-evoked release was unchanged. These findings suggest ADGRL3 modulates dopamine release in complex ways via different pre- and postsynaptic mechanisms.

neuroscience↗

bioRxiv2025

A high-quality bread wheat genome unravels adaptive evolution of wheat end-use quality

Understanding the genetics of superior dough performance is essential for improving wheat end-use quality. Here, we presented a de novo assembly of the genome of JM44, a Chinese wheat cultivar known for its exceptional end-use quality. The JM44 genome achieved reference-level quality (QV = 66.74), depicting a complete picture of complex regions containing gluten genes. Our microsynteny analysis across the Triticum-Aegilops complex showed that high-molecular-weight glutenin subunits (HMW-GSs) loci are highly conserved, while low-molecular-weight glutenin subunits (LMW-GSs) and -/{beta}-gliadins exhibited greater structural variation. These variable loci appear to have been preferentially selected by humans and contributed substantially to the evolution of wheat quality traits. Moreover, we observed that epistatic interactions between gluten genes are strong in modern cultivars, but markedly weaker in landraces, indicating the importance of epistatic selection during modern breeding. Our findings shed light on the genomics and evolution of wheat quality traits, providing valuable guidance for future breeding efforts.

genomics↗

bioRxiv2025

Sea-ice microbial community succession and the potential role of parasitoids in the maintenance of diversity

Sea ice is a crucial, yet declining, habitat in high latitude ecosystems. Here we present a high-temporal resolution amplicon sequence data set collected during the spring ice-algal bloom near Utqia[g]vik, Alaska in 2021 to study sea-ice microbial dynamics. The ice-algal bloom peaked on May 8th, reaching 46.6 mg chlorophyll a m-2, and thereafter became limited by nitrate availability. A massive bloom of the oil-degrading bacterium, Oleispira (>80% relative abundance), coincided with the algal bloom raising questions about hydrocarbon exposure. The sea-ice algal bloom was dominated by diatoms, particularly Nitzschia spp., and transitioned into a flagellate dominated post-bloom community which aligned with melt-associated changes to the physicochemical environment. We explored the relationship between putative parasitoids, Chytridiomycetes, Thecofilosea (Cercozoa), Oomycetes, Syndiniales (Dinoflagellata), and Labyrinthulomycetes (Bigyra), and potential microalgal hosts. Chytrids peaked periodically suggesting synchronized infections and Cryothecomonas (Thecofilosea) was observed parasitizing Nitzschia spp. for the first time in Arctic sea ice. Co-occurrence analysis suggested that diatoms, especially Nitzschia, were the primary hosts of Pacific-Arctic parasitoids, and that top-down parasitoid control may dramatically alter community composition over short timescales, such as days. These results provide important insights into the drivers of spring bloom timing and maintenance of microalgal diversity in sea ice.

microbiology↗

bioRxiv2025

Brainwide genetic capture for conscious state transitions

Neural circuits underlying unconsciousness remain poorly defined. We test the hypothesis that unconsciousness arises from specific, distributed circuits using general anesthesia in mice as a reproducible model. We identify a cortical-to-subcortical shift in neural activity during isoflurane anesthesia that is organized into nine discrete functional communities mapped at single-cell resolution. The lateral parabrachial nucleus (LPB) emerges as a central hub, exhibiting high interconnectivity, spontaneous firing under anesthesia, and preferential recruitment during reactivation of the brain-wide ensemble confirmed by single unit recordings. Chemogenetic reactivation of the captured brain-wide ensemble induces sedation, slow wave oscillations, hypothermia, and analgesia, which are components of anesthesia-induced unconsciousness. Reactivation of the LPB ensemble alone recapitulates a subset of these effects. Together, we define a global neural substrate for unconsciousness and recapitulate its dissociable autonomic, neurophysiologic, and behavioral effects using brain-wide ensemble manipulations. These results establish a neural circuit framework for anesthesia-induced unconsciousness in the mammalian brain.

neuroscience↗

bioRxiv2025

Comparative molecular landscapes of immature neurons in the mammalian dentate gyrus across species reveal special features in humans

Immature dentate granule cells (imGCs) arising from adult hippocampal neurogenesis contribute to plasticity, learning and memory, but their evolutionary changes across species and specialized features in humans remain poorly understood. Here we performed machine learning-augmented analysis of published single-cell RNA-sequencing datasets and identified macaque imGCs with transcriptome-wide immature neuronal characteristics. Our cross-species comparisons among humans, monkeys, pigs, and mice showed few shared (such as DPYSL5), but mostly species-specific gene expression in imGCs that converged onto common biological processes regulating neuronal development. We further identified human-specific transcriptomic features of imGCs and demonstrated functional roles of human imGC-enriched expression of a family of proton-transporting vacuolar-type ATPase subtypes in development of imGCs derived from human pluripotent stem cells. Our study reveals divergent gene expression patterns but convergent biological processes in the molecular characteristics of imGCs across species, highlighting the importance of conducting independent molecular and functional analyses for adult neurogenesis in different species.

neuroscience↗

bioRxiv2024

Colchicine Inhibits Smooth Muscle Cell Phenotypic Switch and Aortic Dissection in Mice

Aortic dissection is a serious cardiovascular disease characterized by intimal tearing and vascular delamination. Smooth muscle cell phenotypic transformation, extracellular matrix degradation and vascular inflammation are the main pathogenic mechanisms of aortic dissection. Colchicine is an alkaloid derived from the plant Colchicum autumnale L. and was the first FDA-approved anti-inflammatory drug in the cardiovascular field. In this study, we investigated the protective effects of colchicine in aortic dissection in mice and found that colchicine resisted aortic dissection by inhibiting vascular inflammation and smooth muscle cell phenotypic transformation, and that colchicine reversed smooth muscle cell phenotypic transformation by targeting the transcriptional activator myocardin. This study provides new directions for the development of drug therapies for aortic dissection.

molecular biology↗

bioRxiv2024

Neuregulin-1 Attenuates Myocardial Ischemia/Reperfusion Injury by Activating the UCP2/PINK1/LC3B-mediated Mitophagy

BACKGROUNDIschemia/reperfusion (I/R) injury may significantly affect the treatment outcomes and prognosis of patients with acute myocardial infarction following coronary artery recanalization. Available evidence suggests that neuregulin-1 (NRG-1) can provide a protection against myocardial I/R injury and is involved in various cardioprotective interventions by potential regulation of mitophagy. However, the molecular mechanisms linking NRG-1 and mitophagy remain to be clarified. This experiment aimed to determine whether NRG-1 postconditioning attenuated myocardial I/R injury through the regulation of mitophagy and to explore the underlying mechanisms. METHODBoth an in vivo myocardial I/R injury model of rats and an in vitro hypoxia/reoxygenation (H/R) model of H9C2 cardiomyocytes were applied. NRG-1 treatment was conducted immediately after I/R or H/R intervention. In the in vivo experiment, cardioprotective effects of NRG-1 were determined by infarct size, cardiac enzyme and histopathologic examinations. The potential downstream pathways and molecular targets of NRG-1 were screened by the RNA sequencing and the Protein-Protein Interaction Networks (PPI). The expression levels of mitochondrial uncoupling protein 2 (UCP2) and mitophagy-related protein in both the I/R myocardium and H/R cardiomyocytes were measured by immunofluorescence staining and Western blots. The activation of mitophagy was observed with the transmission electron microscopy (TEM) and JC-1 staining. RESULTSThe KEGG and GSEA analyses showed that the mitophagy-related pathways were enriched in the I/R myocardium treated with NRG-1, and UCP2 exhibited a significant correlation between mitophagy and interaction with PINK1. Meanwhile, the treatment with mitophagy inhibitor Mdivi-1 significant eliminated the cardioprotective effects of NRG-1 postconditioning in vivo, and the challenge with UCP2 inhibitor genipin could also attenuate the activating effect of NRG-1 postconditioning on mitophagy. Consistently, the in vitro experiment using H9C2 cardiomyocytes showd that NRG-1 treatment significantly up-regulated the expression levels of UCP2 and mitophagy-related proteins, and activated the mitophagy, whereas the challenge with small interfering RNA (siRNA)-mediated UCP2 knockdown abolished the effects of NRG-1. CONCLUSIONSNRG-1 postconditioning can produce a protection against the myocardial I/R injury by activating mitophagy through the UCP2/PINK1/LC3B signaling pathway.

molecular biology↗

bioRxiv2024

Latent-TGF-β has a domain swapped architecture

The multifunctional cytokine TGF-{beta} is produced in a latent form (L-TGF-{beta}) where a RGD containing homodimeric prodomain forms a "ring" encircling mature TGF-{beta} shielding it from its receptors. Thus L-TGF-{beta} must be activated to function, a process driven by dynamic allostery resulting from integrin binding the L-TGF-{beta} RGD motif. Here we provide critical evidence that defines a domain-swapped architecture of L-TGF-{beta}, an essential component in the dynamic allostery mechanism of L-TGF-{beta} activation.

biophysics↗

bioRxiv2024

Impact of carbamate and pyrethroid pesticides on bile acid profiles in an in vitro gut microbiota model

The impact on the microbial community following exposure to commonly used pesticides has recently gained increasing interest. In this study, effects of selected carbamates (carbofuran, aldicarb) and pyrethroids (cypermethrin and cyhalothrin) on gut microbiota and related bile acid metabolism were quantified using a 24 h in vitro fermentation model system with mice feces. The results obtained reveal a pesticide induced significant increase the ratio of secondary over primary bile acids, particularly resulting from the enrichment of {beta}-muricholate ({beta}MCA) accompanied by the depletion of {omega}-muricholate ({omega}MCA). Besides, the bacterial profile showed significantly increased richness of Eggerthellaceae after 24 h exposure to carbofuran and cyhalothrin, and the genera Enterorhabdus belonging to Eggerthellaceae was found to be highly correlated to the fecal bile acid profile. In conclusion, in an in vitro gut microbial model carbamates and pyrethroids caused alterations of the gut microbial community resulting in the modulation of bile acid transformation. This illustrates that the gut microbiota and its metabolism may be a novel target to consider in future pesticide safety evaluations.

microbiology↗

bioRxiv2024

Network-driven identification of indisulam neo-substrates for targeted protein degradation

Indisulam, a DCAF15-based molecular glue degrader, induces widespread proteome changes with implications for cell division and chromosome segregation. While RBM39 and RBM23 are two well-characterized indisulam neo-substrates, additional targets likely exist. To identify those degradation targets, we applied a network-based approach to prioritize novel neo-substrates from large-scale omics data. Our approach integrates proteome-wide expression measurements with information from publicly accessible databases into a multiplex heterogeneous network. Utilizing a Random Walk with Restart algorithm, we identified a preliminary list of 30 neo-substrates. These proteins are likely interactors with DCAF15 in the presence of indisulam and are subject to subsequent degradation. Experimental validation of RBM5, one of the shortlisted candidates, confirmed its degradation in a proteasome-dependent manner, supporting its identification as a novel indisulam neo-substrate. Our work employs established network resources and analytical methods to effectively identify direct targets of indisulam molecular glue degrader. This approach is readily adaptable for exploring novel targets across other molecular glue systems, enhancing its applicability and value to the drug discovery community. SummaryMolecular glue neo-substrate identification via network analysis and proteomics profiling

bioinformatics↗

bioRxiv2024

Molecular Magnetic Resonance Imaging of Dysregulated Zinc Secretion Detects Early Pancreatic Ductal Adenocarcinoma Lesions and Response to KRASG12D Inhibitor Treatment

Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal cancer, primarily due to late-stage diagnosis and limited treatment options. Zinc homeostasis is markedly dysregulated in PDAC and this dysregulation can be probed by administering a secretagogue to stimulate zinc secretion (SSZS) in the exocrine pancreas and imaging this secretion with a zinc sensitive MRI probe. This study demonstrates the potential of SSZS MRI for early detection, monitoring treatment response, and assessing recurrence after treatment withdrawal in PDAC. Our approach relies on interrogating the pancreas, circumventing the challenge of locating small, elusive tumors. By SSZS MRI, we detected PDAC by observing the unique zinc hypersecretory activity of the pancreas when malignancy is present. We observed dysregulation of zinc transporters in both human and mouse pancreas containing PDAC and confirmed secretagogue-stimulated zinc secretion in vitro and in vivo. We found that combining secretagogues such as secretin and caerulein maximized zinc secretion and as such MRI signal in the pancreas. Notably, SSZS MRI detected treatment responses to KRAS G12D inhibition within 3-5 days and identified cancer recurrence as early as one day post-treatment withdrawal. Additionally, secretagogue stimulation improved treatment responses and delayed recurrence in both treatment models. These findings suggest that SSZS MRI could significantly enhance PDAC diagnosis and management, providing a novel, non-invasive imaging modality to improve patient outcomes. STATEMENT OF SIGNIFICANCEThis study demonstrates the utility of secretagogue-stimulated zinc secretion (SSZS) MRI in detecting pancreatic ductal adenocarcinoma (PDAC) at early stages, monitoring treatment responses, and assessing cancer recurrence, thereby offering a promising non-invasive imaging modality to improve PDAC patient management and outcomes.

cancer biology↗

bioRxiv2024

Effects of lambda-cyhalothrin on gut microbiota and related bile acid metabolism in mice

BackgroundSince the gut microbiota plays a crucial role in host metabolism and homeostasis, its alterations induced by xenobiotics, such as pesticides, could pose a risk to host health. Our previous in vitro fermentation study showed that pyrethroid pesticides could affect the mouse bacterial community and related bile acid profiles. Hence in the present study, the effects of the selected pyrethroid lambda-cyhalothrin on the intestinal microbial community and its related bile acid metabolism were evaluated in male and female mice. ResultsThe total amount of bile acids in plasma and fecal samples from lambda-cyhalothrin treated mice markedly increased compared to controls, which could be mainly ascribed to the significantly raised proportions of taurine conjugated bile acids in plasma, and the increase in fecal secondary bile acids. In gut microbial profiles, a significantly increased richness of Prevotellacea and a depletion of Lachnospiraceae were found at the family level upon the treatment with lambda-cyhalothrin. ConclusionTreatment of mice with lambda-cyhalothrin affected the gut microbiota with accompanying changes in bile acid homeostasis. The effects on fecal bile acid profiles were in line with those previously observed in our in vitro study and corroborate that pyrethroid pesticides could affect gut microbiota and related bile acid profiles.

microbiology↗

bioRxiv2024

A simple in vitro fermentation model to detect alterations in gut microbiota-dependent bile acid profiles

A previous in vivo study showed that lincosamide antibiotics (lincomycin and clindamycin) could induce changes in the gut bacterial community, leading to significant changes in fecal bile acid profiles. Herein, our aim is to develop an animal alternative in vitro model for studying gut microbiota-dependent bile acid profiles induced by xenobiotics. The effects of lincosamides were evaluated using this model, and results obtained were verified by comparing with those of the previous in vivo study. Fecal sample processing and bile acid incubation conditions were developed and optimized using feces collected from Wistar rats, and prepared samples were incubated for 24 h with or without lincosamides. Upon treatment of the fecal gut microbiota with lincosamides primary and secondary bile acids showed obviously increased and decreased levels respectively. Moreover, the changes in bile acid profile could be linked to a reduced richness of family Erysipelotrichaceae, Bacteroidacea and Lactobacillaceae or Prevotellaceae. The consistent consequences of in vivo and in vitro provides a proof of principle for further application on elucidating effects of other xenobiotics on the gut bacterial community and related bile acid metabolism, thereby contributing to the 3Rs (replacement, reduction and refinement) in animal testing.

biochemistry↗

bioRxiv2024

CRISPR-mediated chromosome deletion facilitates genetic mapping of Vip3Aa resistance gene within complex genomic region in an invasive global pest

Connecting genetic variation to phenotypes and understanding the underlying biological mechanisms has been a fundamental goal of biological genetics. Here, we used the association analysis to identify a Vip3Aa resistance-associated genomic region in a strain of fall armyworm, JC-R, which exhibits >5000-fold resistance to the Bt toxin Vip3Aa. However, through various analytical approaches and fine-scale mapping across different populations, we demonstrated that this genomic region exhibits strong genetic linkage. The chromosome-level genome of JC-R and its parent strain JC-S were assembled, and extensive structural variations in the linkage regions were identified, which could be responsible for maintaining the linkage. To identify the causal variation within this linked region, a chromosome fragment stepwise knockout strategy based on CRISPR/Cas9 was developed. By crossing with the resistant strain and phenotyping segregating offspring on Vip3Aa-containing diet, we identified a chromosomal segment, KO8, containing the resistant gene. Subsequently, we conducted a comprehensive analysis of the variations in the KO8 region using multi-omics approaches, including genomic data, RNA-seq, proteomic, PacBio long read Iso-seq, and phosphoproteomic data. This analysis identified multiple variations in the chitin synthase gene CHS2, including amino acid substitution, alternative splicing, and changes in phosphorylation sites. After knocking out the CHS2, larvae exhibited over 6777-fold resistance to Vip3Aa. These results demonstrate that the chromosome fragment stepwise knockout strategy is a viable approach for studying complex genomic regions, and highlight the value of comprehensive analysis of genetic variations using multi-omics data. The identified candidate gene could potentially advance monitoring and management of pest resistance to Vip3Aa.

genetics↗

bioRxiv2024

A SMARTR workflow for multi-ensemble atlas mapping and brain-wide network analysis

In the last decade, activity-dependent strategies for labelling multiple immediate early gene (IEG) ensembles in mice have generated unprecedented insight into the mechanisms of memory encoding, storage, and retrieval. However, few strategies exist for brain-wide mapping of multiple ensembles, including their overlapping population, and none incorporate capabilities for downstream network analysis. Here, we introduce a scalable workflow to analyze traditionally coronally-sectioned datasets produced by activity-dependent tagging systems. Intrinsic to this pipeline is simple multi-ensemble atlas registration and statistical testing in R (SMARTTR), an R package which wraps mapping capabilities with functions for statistical analysis and network visualization, and support for import of external datasets. We demonstrate the versatility of SMARTTR by mapping the ensembles underlying the acquisition and expression of learned helplessness (LH), a robust stress model. Applying network analysis, we find that exposure to inescapable shock (IS), compared to context training (CT), results in decreased centrality of regions engaged in spatial and contextual processing and higher influence of regions involved in somatosensory and affective processing. During LH expression, the substantia nigra emerges as a highly influential region which shows a functional reversal following IS, indicating a possible regulatory function of motor activity during helplessness. We also report that IS results in a robust decrease in reactivation activity across a number of cortical, hippocampal, and amygdalar regions, indicating suppression of ensemble reactivation may be a neurobiological signature of LH. These results highlight the emergent insights uniquely garnered by applying our analysis approach to multiple ensemble datasets and demonstrate the strength of our workflow as a hypothesis-generating toolkit.

neuroscience↗

bioRxiv2024

Co-Transplantation-Based Human-Mouse Chimeric Brain Models to Study Human Glial-Glial and Glial-Neuronal Interactions

Human-mouse chimeric brain models, generated by transplanting human induced pluripotent stem cell (hiPSC)-derived neural cells, are valuable for studying the development and function of human neural cells in vivo. Understanding glial-glial and glial-neuronal interactions is essential for unraveling the complexities of brain function and developing treatments for neurological disorders. To explore these interactions between human neural cells in vivo, we co-engrafted hiPSC-derived neural progenitor cells together with primitive macrophage progenitors into the neonatal mouse brain. This approach creates human-mouse chimeric brains containing human microglia, macroglia (astroglia and oligodendroglia), and neurons. Using super-resolution imaging and 3D reconstruction techniques, we examine the dynamics between human neurons and glia, and observe human microglia pruning synapses of human neurons, and often engulfing neurons themselves. Single-cell RNA sequencing analysis of the chimeric brain uncovers a close recapitulation of the human glial progenitor cell population, along with a dynamic stage in astroglial development that mirrors the processes found in the human brain. Furthermore, cell-cell communication analysis highlights significant neuronal-glial and macroglial-microglial interactions, especially the interaction between adhesion molecules neurexins and neuroligins between neurons and astroglia, emphasizing their key role in synaptogenesis. We also observed interactions between microglia and astroglia mediated by SPP1, crucial for promoting microglia growth and astrogliosis, and the PTN-MK pathways, instrumental in homeostatic maintenance and development in macroglial progenitors. This innovative co-transplantation model opens up new avenues for exploring the complex pathophysiological mechanisms underlying human neurological diseases. It holds particular promise for studying disorders where glial-neuronal interactions and non-cell-autonomous effects play crucial roles.

neuroscience↗

bioRxiv2024

Intersectin1 promotes clathrin-mediated endocytosis by organizing and stabilizing endocytic protein interaction networks

During clathrin-mediated endocytosis (CME), dozens of proteins are recruited to nascent CME sites on the plasma membrane. Coordination of endocytic protein recruitment in time and space is important for efficient CME. Here, we show that the multivalent scaffold protein intersectin1 (ITSN1) promotes CME by organizing and stabilizing endocytic protein interaction networks. By live-cell imaging of genome-edited cells, we observed that endogenously labeled ITSN1 is recruited to CME sites shortly after they begin to assemble. Knocking down ITSN1 impaired endocytic protein recruitment during the stabilization stage of CME site assembly. Artificially locating ITSN1 to the mitochondria surface was sufficient to assemble puncta consisting of CME initiation proteins, including EPS15, FCHO, adaptor proteins, the AP2 complex and epsin1 (EPN1), and the vesicle scission GTPase dynamin2 (DNM2). ITSN1 can form puncta and recruit DNM2 independently of EPS15/FCHO or EPN1. Our work redefines ITSN1s primary endocytic role as organizing and stabilizing the CME protein interaction networks rather than a previously suggested role in initiation and provides new insights into the multi-step and multi-zone organization of CME site assembly.

cell biology↗

bioRxiv2024

ProLLM: Protein Chain-of-Thoughts Enhanced LLM for Protein-Protein Interaction Prediction

The prediction of protein-protein interactions (PPIs) is crucial for understanding biological functions and diseases. Previous machine learning approaches to PPI prediction mainly focus on direct physical interactions, ignoring the broader context of nonphysical connections through intermediate proteins, thus limiting their effectiveness. The emergence of Large Language Models (LLMs) provides a new opportunity for addressing this complex biological challenge. By transforming structured data into natural language prompts, we can map the relationships between proteins into texts. This approach allows LLMs to identify indirect connections between proteins, tracing the path from upstream to downstream. Therefore, we propose a novel framework ProLLM that employs an LLM tailored for PPI for the first time. Specifically, we propose Protein Chain of Thought (ProCoT), which replicates the biological mechanism of signaling pathways as natural language prompts. ProCoT considers a signaling pathway as a protein reasoning process, which starts from upstream proteins and passes through several intermediate proteins to transmit biological signals to downstream proteins. Thus, we can use ProCoT to predict the interaction between upstream proteins and downstream proteins. The training of ProLLM employs the ProCoT format, which enhances the models understanding of complex biological problems. In addition to ProCoT, this paper also contributes to the exploration of embedding replacement of protein sites in natural language prompts, and instruction fine-tuning in protein knowledge datasets. We demonstrate the efficacy of ProLLM through rigorous validation against benchmark datasets, showing significant improvement over existing methods in terms of prediction accuracy and generalizability. Our results highlight the potential of LLMs to transform the field of PPI, serving as a robust potential tool for various categories of biological and medical research. The code is available at: https://github.com/MingyuJ666/ProLLM.

bioinformatics↗