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Zhang, D.

Publications and source records attributed to Zhang, D..

At least 91 records · Page 5Linked to original sources

Multi-Timescale Neural Adaptation Failure as a Mechanistic Signature of Major Depression

Major depression (MD) is usually characterized in terms of momentary abnormalities, such as negative bias or emotional blunting, derived from paradigms that measure only the first response to a stimulus. Yet depressive experience in daily life is repetitive and cumulative. Here we test the hypothesis that a failure of neural adaptation across repetitions is a core feature of MD. Using a repeated negative-stimulus paradigm, we quantified adaptation at micro (within-trial) and macro (across-session) scales via electroencephalography in 28 MD patients and 34 healthy controls, measuring both conventional event-related potentials and large-scale traveling-wave propagation. MD patients exhibited pervasive maladaptation: neural rigidity at the micro scale (absent repetition suppression) and progressive regulatory depletion at the macro scale (escalating emotional reactivity with declining cognitive control). Across analyses, adaptation-based metrics revealed larger group differences than single-shot indices, and classifiers built on adaptation features--especially traveling-wave dynamics--outperformed single-shot models (task AUC = 0.83 vs 0.78) and generalized to two independent datasets (up to AUC = 0.91). These findings challenge conventional symptom-based characterizations of MD, establishing adaptation failure--not initial reactivity--as the mechanistically primary pathological signature. This reframing provides a unified mechanistic explanation for rumination and cognitive inflexibility while offering a standardized, low-cost biomarker requiring minimal electrodes ([≤]8 channels), enabling large-scale screening in resource-limited settings.

neuroscience↗

VARS1 fuels prostate cancer evolution via codon-selective translational rewiring

Cancers exhibit translatomic alterations, but little is known about the drivers that control translational dysregulation and can also be exploited therapeutically in prostate cancer (PCa). By systematic interrogating a group of genes associated with transfer RNA (tRNA) biology (termed as tRNA biogenesis), here we establish tRNA biogenesis as an overall oncogenic pathway in, and identify valyl-tRNA synthetase (VARS1) as the key underlying driver of, PCa progression. Targeting VARS1 reduces the charged levels of valine tRNAs, inhibits global translation and suppresses aggressive PCa both in vitro and in vivo. Surprisingly, knocking down VARS1 does not preferentially impact on translation of valine-rich transcripts, but instead switches the usage of PCa-preferred GTA and GTT codons to GTC and GTC codons, which are optimal in normal prostates. Mechanistically, overexpressed VARS1 in PCa selectively accelerates the translation of genes with high GTA and GTT codon content that are functionally tied to cell mitosis and cancer-promoting pathways. Dietary valine restriction (VR) reduces global translation and slows the growth of both AR+ and AR--xenograft models. We have also developed a VARS1 inhibitor that suppresses autochthonous prostate tumours by targeting its aminoacylation activity. Altogether, our studies indicate that VARS1 acts as an oncogene promoting PCa progression through codon-selective translational rewiring, and therefore represents a therapeutic target susceptible to dietary VR and small molecule therapy.

cancer biology↗

ERAD Activity Distinguishes the Functional Heterogeneity of Hematopoietic Stem Cells

Hematopoietic stem cells (HSCs) rely on precisely controlled proteostasis to sustain lifelong self-renewal, yet whether intrinsic proteostatic characteristics can prospectively define functional diversity within the HSC pool remains unknown. In this study, we developed a dual-fluorescence reporter system to visualize endoplasmic reticulum-associated degradation (ERAD) activity in vivo and discovered that ERAD activity can prospectively predicts the long-term reconstitution potential of HSCs. Remarkably, ERAD states were maintained through self-renewal, revealing an inheritable "proteostatic memory" within the HSC pool. Transcriptomic and functional analyses identified SOCS2 as a key regulator of this process: SOCS2 inhibits JAK2 signaling to sustain ERAD activity, whereas hyperactive JAK2 interacts with the ERAD E3 ligase Hrd1 and suppresses VCP-mediated misfolded substrate. These findings define a SOCS2-JAK2-ERAD axis that connects cytokine signaling to intrinsic proteostasis remodeling, establishing ERAD activity as a predictive and heritable marker of HSC function and providing a conceptual framework for understanding hematopoietic stem cell heterogeneity.

cell biology↗

Noninvasive enrichment of circulating tumor biomarkers in a mouse model of diffuse midline glioma using focused ultrasound

BackgroundDiagnosing diffuse midline glioma (DMG) through invasive tissue biopsies is challenging due to the tumors eloquent location at the pons. Liquid biopsies offer a promising noninvasive alternative; however, their limited detection sensitivity and lack of information on the source of biomarkers pose great challenges. This study aimed to evaluate the feasibility and safety of using focused ultrasound (FUS) with microbubbles to enrich circulating DMG tumor biomarkers in blood and cerebrospinal fluid (CSF) using a mouse model. MethodsMurine DMG cells, transfected with enhanced green fluorescent protein (EGFP) and firefly luciferase (Fluc) genes, were orthotopically injected into the mouse brain. Magnetic resonance imaging was used to guide FUS targeting of the DMG tumor. Droplet digital PCR assays were developed to detect circulating tumor DNA (ctDNA) and RNA (ctRNA) of EGFP and Fluc in blood and CSF samples collected after FUS. ResultsFUS enhanced the plasma levels of EGFP ctRNA by 5.4-fold (p=0.0112), compared with liquid biopsy without FUS. CSF EGFP ctDNA was increased by 2.5-fold (p=0.0253), and Fluc ctDNA was increased by 2.6-fold (p=0.0253) with FUS. No brain tissue damage was associated with FUS sonication. ConclusionsThis study demonstrated the feasibility and safety of FUS in enriching tumor biomarkers in blood and CSF in a mouse model of DMG. The enrichment ratio for circulating biomarkers depends on the source (plasma vs. CSF), analyte type (ctDNA vs. ctRNA), and individual marker (EGFP vs. Fluc). These findings support the potential future application of FUS to advance the diagnosis of DMG through liquid biopsy. Key pointsO_LIddPCR assays were developed to detect plasma and CSF ctDNA and ctRNA in a mouse model of DMG C_LIO_LIFUS with microbubbles enriched ctDNA and ctRNA in the blood and CSF of a mouse model of DMG C_LIO_LIThe enrichment ratio on circulating biomarkers is dependent on the source (plasma vs. CSF), analyte type (ctDNA vs. ctRNA), and individual marker (EGFP vs. Fluc) C_LI Importance of the studyLiquid biopsy via detecting circulating tumor biomarkers holds enormous clinical value in the diagnosis of diffuse midline glioma (DMG), where the eloquent location of the tumor poses significant risks to invasive surgical tissue biopsies. However, the effectiveness of liquid biopsy is hindered by its low sensitivity and the lack of information about the source of biomarkers. This study demonstrated that noninvasive and spatially targeted FUS treatment can release tumor-derived DNA and RNA into the blood and CSF in a mouse model of DMG. This study also found that the enrichment effect of FUS on circulating biomarkers depends on the source (plasma vs. CSF), analyte type (ctDNA vs. ctRNA), and individual marker (EGFP vs. Fluc). This study opens new avenues for advancing noninvasive DMG diagnosis through FUS-enhanced liquid biopsy (sonobiopsy).

bioengineering↗

The Human Hippocampus Is Involved in Auditory Short-Term Memory Trace Formation

The human hippocampus has been claimed to play an important role in long-term memory, or episodic memory, but its contribution to short-term memory remains debated. Here, we demonstrate human hippocampal involvement in auditory short-term memory (ASTM) trace formation. We used a classic oddball paradigm and intracranial recordings across various human brain areas. High frequency activities evoked by deviant stimuli in subjects indicate the generation of ASTM trace. Analysis of auditory response latencies across the hippocampus, insula, and temporal, parietal, and frontal lobes revealed the early processing of ASTM trace at a pre-attention stage. Granger causality analysis further showed that ASTM trace processing engages hierarchical cortical areas and clarified their interactions. Bottom-up signals flow from the insula and auditory temporal regions to the frontal lobe early on, followed by top-down information from the frontal lobe to the hippocampus, inferior temporal lobe, and insula at a later pre-attentive stage. Critically, Bayesian model selection of dynamic causal modeling revealed that deviant stimuli selectively enhanced the effectiveness of top-down connections to the hippocampus, thereby facilitating ASTM trace formation. These results provide compelling evidence that the human hippocampus contributes to auditory short-term memory at a pre-attention stage and suggests a challenge to entrenched beliefs in the classification of memory systems.

neuroscience↗

KDM7-mediated oxygen sensing reprograms chromatin to enhance hypoxia tolerance in the root

Roots frequently encounter low oxygen (hypoxia) from soil compaction or water saturation and must adapt to this stress. We investigated how root tip cells sense hypoxia and adjust the meristem epigenome to activate genes that promote tolerance and growth under oxygen limitation. In Arabidopsis root tips, hypoxia tolerance was linked to increased trimethylation of histone H3 at lysine 4 (H3K4me3). We also found that group 7 demethylases (KDM7s) are directly inhibited by hypoxia, and that genetic inactivation of KDM7s, like hypoxia, induces expression of genes essential for meristem survival under oxygen deprivation. We propose that KDM7s function as root-specific oxygen sensors that prime and support hypoxia tolerance.

plant biology↗

WormSpot: a machine learning-powered viability scoring platform in C. elegans for Candida pathogenicity studies

Invasive Candida infections pose a critical health challenge, exacerbated by emerging antifungal resistance. Caenorhabditis elegans (C. elegans) offers a genetically tractable and scalable model for studying Candida pathogenicity, yet conventional viability assays remain labor-intensive, limiting high-throughput applications. In this study, we developed a machine learning-driven worm viability scoring platform, WormSpot, using representative images of Candida-infected worm and the robust YOLOv8-based framework. By analyzing static morphological features, our model accurately classifies worm viability post-infection, achieving strong concordance with manual scoring while requiring minimal image input. Validation with well-characterized Candida albicans mutants and antifungal agents confirms the platforms robustness in predicting worm survival trends. Notably, WormSpot performs efficiently with diverse image formats and is compatible with standard multi-well microscopy workflows, enabling automated data analysis and scalable application in various experimental setups. In conclusion, WormSpot provides a data-efficient, reproducible tool for assessing Candida virulence using C. elegans, supporting both basic pathogenicity study and antifungal discovery in high-throughput settings.

bioinformatics↗

"Awe-scillations": EEG spectral and complexity representations of awe

Awe is a positive emotion often accompanied by sensations of vastness and unity, with known benefits for well-being and social behavior. However, its neural underpinnings remain poorly understood. We recorded electroencephalography (EEG) and autonomic physiology in 23 healthy older participants while they watched a nature-based audiovisual film and subjectively rated awe events. Awe was the predominant emotion reported - though other positive emotions (e.g., joy) were also highly rated. Awe events were associated with decreased skin conductance level (SCL), and decreased EEG alpha and theta spectral power - physiological changes associated with low arousal and positively valenced emotional states. Interestingly, awe events exhibited increased Lempel Ziv Complexity (LZC) - indicating heightened neural signal entropy and increased richness of the conscious experience. LZC was also positively associated with the intensity of the awe ratings and negatively associated with SCL. Three additional datasets with separate independent induction methods (video clips and pharmacological induction via N,N-dimethyltryptamine) also showed positive occipital LZC associations with awe - suggesting some generalizability of LZC as a neurophysiological marker of awe. These results suggest that awe evokes neurophysiological states linked to the subjective affective experience. Impact StatementAwe, an emotion of increasing interest, has been studied with fMRI and peripheral physiology - but few studies have used electroencephalography (EEG). In this EEG study, we utilize a movie-watching paradigm to explore potential physiological correlates of awe. The results present EEG-based complexity increases as a potential correlate of awe, though showing limited generalization to independent datasets and limited uniqueness compared to joy, another positive emotion.

neuroscience↗

A Syngeneic Immunocompetent Mouse Model of Gallbladder Cancer Reveals Tumorigenesis and Therapeutic Response

PurposeGallbladder cancer (GBC) is a rare but highly lethal malignancy with one of the poorest prognoses among cancers of the digestive system cancers. However, current experimental models of GBC face critical limitations, particularly their dependence on immunodeficient hosts, which precludes the investigation of the tumor microenvironment. We aimed to establish a novel syngeneic immunocompetent mouse model that recapitulates human GBC and enables the investigation of tumor-immune interactions. Experimental DesignWe engineered a murine cell line (mGBC1-ZH) from normal mouse gallbladder organoids expressing Kras and Trp53 (encoding mouse p53) mutations. Tumorigenic potential of mGBC1-ZH was evaluated by subcutaneous and orthotopic implantation. RNA-Seq and WES was used to demonstrate its characterization and similarity with human GBC. Immunohistochemistry, CCK8, and transwell assays wereused to investigate the role of CXCL5 in GBC. Therapeutic responses to standard first-line chemotherapeutic agents was evaluated in the syngeneic GBC model. ResultsThis model supports both subcutaneous and orthotopic tumor growth in immunocompetent C57BL/6J hosts while preserving hallmark features of human GBC, including biliary epithelial differentiation (CK7+/CK19+), aggressive histopathology, and an immunosuppressive "cold" tumor microenvironment. Genomic characterization revealed recurrent chromosomal instability and copy number alterations mirroring human GBC. Comprehensive transcriptomic profiling revealed profound gene expression changes during the model development, and resembled transcriptional features between mGBC1-ZH and human GBC cell lines and samples. CXCL5 was found to be upregulated in human GBC, and promote proliferation, metastasis, and neutrophils infiltration of GBC in the syngeneic mouse model. Functional validation of the syngeneic GBC model demonstrated therapeutic responsiveness to frontline chemotherapeutics gemcitabine and cisplatin with significant in vivo tumor regression. ConclusionsIn summary, we establised a novel syngeneic GBC mouse model, overcoming the limitations of traditional models by enabling studies in immunocompetent hosts. This model provides valuable insights into the molecular evolution from normal gallbladder cells to transformed cancer cells and establishes a robust platform for both mechanistic studies and therapeutic development.

cancer biology↗

AI-HEAD: Auto-indexing for Helical assembles' diffraction and fast dynamic structure determination

Analyzing the structure of the helical assembly is very important to excavate the mechanism of base life activities such as cell morphology maintaining, cargo transportation, et. al. However, the structure determination of helical assembles still challenging due to ambiguous of helical parameters. Here, we developed automatic, fast and accurate helical parameter and structure calculation method AI-HEAD, which perform diffraction indexing and parameter calculation automatically in seconds, and determine the final structure unambiguously by sorting parameters semi-automatically. AI-HEAD is open source and also provides a user-friendly graphical interface.

biophysics↗

Hydrogen sulfide modulates plant hypoxic responses through the persulfidation of Plant Cysteine Oxidases

Hydrogen sulfide (H2S) is a gaseous molecule historically regarded as toxic. Nevertheless, increasing evidence has brought to light important physiological roles in both animals and plants. In plants, H2S is involved in environmental and developmental responses, such as stomatal closure and seed germination, and in tolerance mechanisms to different stress conditions like salinity, drought and waterlogging. In this study, we report a function of H2S as a modulator of hypoxic responses in Arabidopsis thaliana. A combination of biochemical and genetic evidence demonstrates that H2S inhibits the activity of Plant Cysteine Oxidases, the molecular sensors of oxygen, through protein persulfidation to modulate hypoxia-associated responses. Furthermore, we show that H2S physiology contributes to responses to low oxygen, as disturbing H2S production impaired activation of hypoxia-responsive genes and submergence tolerance. Overall, this work introduces H2S as signalling modulator in plant hypoxic responses and adds a regulatory layer to the plant oxygen-sensing mechanism.

plant biology↗

Generation and validation of an aryl hydrocarbon receptor knockout human embryonic stem cell line

Glucose homeostasis is tightly controlled by hormones secreted from pancreatic islets. The most abundant cell type in islets is the {beta}-cell, which secretes insulin in response to nutritional stimuli. We previously reported that the adverse metabolic effects of high-dose dioxin exposure in mice are regulated by the aryl hydrocarbon receptor (AHR) specifically in {beta}-cells. Additionally, fetal exposure to low-dose dioxin reduced {beta}-cell area in female mice at birth; however, the role of AHR in {beta}-cell development has not been explored. To characterize the AHR pathway in developing human {beta}-cells, we differentiated human embryonic stem cells (hESCs) into "islet-like" cell clusters (SC-islets) in vitro and treated cells with vehicle or dioxin for 24-hours at key stages of differentiation. Dioxin exposure robustly upregulated AHR gene targets (CYP1A1, AHRR) at all stages of differentiation but only had modest effects on markers of islet development and maturity. We next generated an AHR knock-out (KO) hESC line and found that basal CYP1A1 expression was profoundly suppressed in AHR-KO cells compared to parental cells at all stages of differentiation. Key markers of developing and mature pancreatic islets were largely unaffected by AHR deletion; however, G6PC2 was consistently downregulated in SC-islets from AHR-KO cells compared to parental cells. Interestingly, AHR-KO SC-islets also showed modestly increased insulin secretion relative to the parental line, suggesting a role for AHR in islet development. This novel AHR-KO cell line will allow for deeper investigation into the impact of AHR on development of human islets and other cell lineages.

developmental biology↗

Single-Cell Immune Profiling Reveals Non-classical Monocyte-Driven Immunodepression in Tuberculosis Treatment Non-Responders

Sputum culture conversion (SCC) at 2 months is a critical predictor of tuberculosis (TB) treatment outcomes, yet the underlying immune alterations driving treatment non-response remain unclear. We performed single-cell RNA sequencing on peripheral blood mononuclear cells from 8 TB patients, stratified by 2-month SCC status, to characterize cellular heterogeneity and intercellular communication. Treatment non-responders exhibited marked expansion and terminal differentiation of non-classical monocytes with elevated TB progression risk signatures. These cells showed reduced outgoing but enhanced incoming signaling, prominently via IL-16 and TRAIL pathways, potentially amplifying regulatory T cell (Treg)-mediated immunosuppression. CD4 Tregs in non-responders engaged in intensified GALECTIN signaling toward CD8 cytotoxic T cells and mature NK cells, contributing to effector cell exhaustion. NK cell subsets, particularly mature NK c2, displayed increased inhibitory receptor expression and terminal differentiation states. Our findings delineate a dysregulated "non-classical monocyte -Treg -cytotoxic lymphocyte" axis in TB treatment failure, highlighting candidate biomarkers and host-directed therapeutic targets.

bioinformatics↗

Reverse transcribed ssDNA derepresses translation of a retron antiviral protein

Retrons are bacterial immune systems that prevent the spread of phages by initiating a toxic response within infected hosts. All previously characterized retrons produce high levels of multicopy single-stranded DNA (msDNA) in the cell by reverse transcription, which acts as an antitoxin in the absence of phage infection. However, we describe here a non-canonical mechanism for Type VI retrons, which do not produce detectable msDNA in the absence of phage, yet still provide phage defense. Focusing primarily on Retron-Vpa2, a Type VI retron from Vibrio parahaemolyticus, we show broad defense against phages and identify triggers of the system within phage recombination systems. Within the Retron-Vpa2 operon, we find a highly enriched, structured transcript that we term a hybrid RNA (hyRNA), which contains both the retrons reverse transcription template and a translationally repressed toxic effector coding sequence. We find that phage infection induces the accumulation of high levels of msDNA and that this msDNA is necessary for derepressing translation of the antiviral toxin. These findings present key biological and mechanistic insights into a distinct group of retrons while highlighting the diversity of systems that participate in bacterial immunity.

microbiology↗

Coordination of local and global responses in individual mouse thalamic local interneurons

Inhibitory interneurons, featuring presynaptic release sites and spiking activity in dendrites, present a puzzle in their signal organization and coordination. We investigated this in local interneurons (LINs) of the primary visual thalamus using two-photon calcium imaging in awake mice with both local and full-screen visual stimuli. Dendrites in single LINs showed consistent global responses to full-screen stimuli but varied responses to local stimuli. Dendrites from the same LIN exhibited different receptive fields that followed retinotopic progression. The similarity between dendritic and somatic responses decreased with increasing distance. Weak local stimuli could excite dendrites locally, while salient local stimuli triggered global responses. Salient global stimuli further enhanced motion selectivity, preference consistency, and peak responses. Thus, LINs leverage both local and global dendritic activation to perform spatially-organized, feature-selective, and size-dependent motion processing, providing new insights into the complexity and precision of sensory processing in the early visual system. HighlightsO_LILocal interneurons (LINs) exhibit diverse yet sharp tuning to moving stimuli. C_LIO_LIdisplay an orderly shift of receptive field centers along their dendrites. C_LIO_LIThe propagation of calcium signals under local stimuli depends on stimulus strength. C_LIO_LIFull-screen stimuli enhance motion selectivity and peak responses. C_LI

neuroscience↗

New proteomic biomarkers identified in plasma extracellular vesicles in sarcoidosis: a case-control matched study

BACKGROUNDSarcoidosis is a heterogeneous disease with unknown mechanisms, nonspecific therapies, and multiple etiologies. The role of blood extracellular vesicles (EVs) in the diagnosis and pathogenesis of sarcoidosis remains obscure. AIMS/OBJECTIVES. This study aims to test the hypothesis that the EV proteins in the blood can serve as phenotypic biomarkers of sarcoidosis. METHODS. We combined EV proteomics with machine learning algorithms to identify and prioritize biomarkers, enrich their functions, and cluster networks in case-control matched ACCESS patients. RESULTS. In total, 278 plasma EV proteins were significantly upregulated or downregulated in 40 sarcoidosis patients compared with 40 matched healthy controls. We identified 97 proteins that could serve as biomarkers with an AUC > 0.75. Of these, the AUC was > 0.90 for 13 proteins. 62 differentially expressed EV proteins strongly correlated with 20 clinical variables of severity, chest X-ray findings, and/or laboratory results. Functional annotation and network analysis suggest that these differentially expressed proteins regulate endocytosis, host responses to external stimuli, and transcription processes. Moreover, the top three ranked pathways were clathrin-mediated endocytosis, Hsp90 chaperone cycle, and spliceosome. CONCLUSIONS. This study demonstrates that plasma EV proteins can serve as biomarkers of various clinical phenotypes of the disease. At a Glance CommentaryCurrent Scientific Knowledge on the Subject: Sarcoidosis is a heterogeneous condition affecting multiple organs. The role of blood extracellular vesicles in the diagnosis and pathogenesis of this condition remains unknown. What This Study Adds to the Field: We identified differentially expressed proteins in plasma EVs by combining proteomics and machine learning algorithms. Top-ranked proteins can serve as diagnostic biomarkers and potential mechanisms for the development of sarcoidosis.

molecular biology↗

Migration patterns and hybridization within the Asian stonechat complex in response to a major geographical barrier

Long-distance avian migration is thought to be under strong natural selection. Facing geographical barriers, migrants display various patterns considered to be adaptive. For example, they may detour along either side around the barrier or cross it, requiring specialized behavioral adaptations. Variations within closely related taxa are excellent sources for understanding the evolutionary background of migration and how barriers are shaping migration routes. In Asia, some species are assumed to have a migratory divide in response to the major geographical barrier, the Qinghai-Tibet Plateau (QTP), including the stonechat taxa (Siberian Stonechat Saxicola maurus maurus and Amur Stonechat S. stejnegeri). As they detour along either side of the QTP, these taxa are believed to disfavor a crossing over the highland. However, the more southernly distributed Tibetan Stonechat (S. m. przewalskii) breeds on the QTP, suggesting adaptation to high elevation. To investigate migration patterns and the potentially associated genetic differences, we studied migration routes and population genetics of four populations around the assumed migratory divide in Russia and Mongolia, and of one from the QTP in China. Our results confirmed the existence of a migratory divide between maurus and stejnegeri, albeit with extensive hybridization. We observed both the hypothesized western and eastern routes, but also found individuals employing intermediate routes crossing the QTP, of which two-thirds were clear hybrids. Meanwhile, przewalskii followed a highland-crossing route and was genetically differentiated from maurus and stejnegeri. The diverse migration routes among Asian stonechats show differential responses towards the geographical barrier. The intermediate route may be associated with hybridization, and its conditional viability may facilitate gene flow between maurus and stejnegeri. The Asian stonechat complex thus offers great opportunities for novel research of the genetics and evolution of migration. The specific evolutionary background associated with inhabiting and crossing the QTP can offer new perspectives in this field. Teaser textMigratory divides can arise in birds because alternative routes around migratory barriers would select for behaviors to restrict hybridization. Hybrids of parental types that employ alternative routes are hypothesized to embark on intermediate routes that would expose them to suboptimal conditions, resulting in post-zygotic reproductive isolation. However, this hypothesis is challenged when a sister taxon actually breeds on the geographical barrier. This is the case in the Asian stonechat complex that breeds near or on the Qinghai-Tibet Plateau (QTP), the roof of the world. We demonstrated a migratory divide in central Siberia to Mongolia for race maurus and stejnegeri, yet showed also evidence for extensive hybridization. Hybrids migrated along a newly discovered intermediate route, seemingly viable and overlaps with the migration trajectory of race przewalskii over the eastern part of the QTP. The Asian migratory divide relative to the QTP thus provided new insights to the evolution of landbird migration.

evolutionary biology↗

Cinematic Simulation of Substrate-to-Product Chemical Reactions with Chemical Accuracy Using QuantaMind MD

Polyethylene terephthalate hydrolases (PETases) are enzymes that catalyze the breakdown of PET plastic. Previous studies have employed classical molecular dynamics (MD) and quantum mechanical/molecular mechanical (QM/MM) simulations to probe the catalytic mechanisms of the PETase-catalyzed reaction. In this work, we apply QuantaMind, a deep learning-based machine learning force field (MLFF) trained on diverse chemical systems and transition-state energies at density functional theory (DFT)-level, to simulate the complete catalytic cycle of the PETase reaction. Our simulations capture key proton transfer events and the stabilization role of the oxyanion hole in PETase, in agreement with previous computational studies, without introducing artificial biases to the interactions. The simulations also provide estimates of free energy barriers for each reaction step with uncertainty estimation, consistent with experimental values and previous QM/MM studies. To our knowledge, this work represents the first complete DFT-level MD simulation of a biomolecular enzymatic reaction using DL-based MLFFs.

biochemistry↗