Biology subjects

Wu, J.

Publications and source records attributed to Wu, J..

At least 361 records · Page 20Linked to original sources

bioRxiv2024

Colorectal Cancer Stem Cell Subtypes Orchestrate Distinct Tumor Microenvironments

SummarySeveral classification systems have been developed to define tumor subtypes in colorectal cancer (CRC). One system proposes that tumor heterogeneity derives in part from distinct cancer stem cell populations that co-exist as admixtures of varying proportions. However, the lack of single cell resolution has prohibited a definitive identification of these types of stem cells and therefore any understanding of how each influence tumor phenotypes. Here were report the isolation and characterization of two cancer stem cell subtypes from the SW480 CRC cell line. We find these cancer stem cells are oncogenic versions of the normal Crypt Base Columnar (CBC) and Regenerative Stem Cell (RSC) populations from intestinal crypts and that their gene signatures are consistent with the "Admixture" and other CRC classification systems. Using publicly available single cell RNA sequencing (scRNAseq) data from CRC patients, we determine that RSC and CBC cancer stem cells are commonly co-present in human CRC. To characterize influences on the tumor microenvironment, we develop subtype-specific xenograft models and we define their tumor microenvironments at high resolution via scRNAseq. RSCs create differentiated, inflammatory, slow growing tumors. CBCs create proliferative, undifferentiated, invasive tumors. With this enhanced resolution, we unify current CRC patient classification schema with TME phenotypes and organization. O_LITwo cancer stem cell subtypes are isolated and determined to be commonly found as mixed populations in human CRC C_LIO_LIThe heterogeneous SW480 cell line models and unifies two binary cancer stem cell classifications of colorectal cancer C_LIO_LIHigh resolution analysis of xenograft tumors reveals that CRC stem cells are dominant, context-independent organizers of their TME C_LIO_LIRSC/YAP/STAT3-positive CRC stem cells create differentiated tumors that attempt tissue generation via an inflammatory, angiogenic, oncofetal program C_LIO_LICBC/MYC-positive CRC stem cells create tumors that are proliferative, undifferentiated, and invasive C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=137 SRC="FIGDIR/small/591144v1_ufig1.gif" ALT="Figure 1"> View larger version (66K): org.highwire.dtl.DTLVardef@166735aorg.highwire.dtl.DTLVardef@11f3e55org.highwire.dtl.DTLVardef@354a4forg.highwire.dtl.DTLVardef@a18ab1_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

Splenic red pulp macrophages eliminate the liver-resistant Streptococcus pneumoniae during bloodstream infection

The spleen is well-known for defense against invasive infections of encapsulated bacteria, particularly Streptococcus pneumoniae (pneumococcus). However, the precise mechanism of the splenic anti-bacterial immunity remains elusive. Here we report that red pulp (RP) macrophages execute the splenic defense against S. pneumoniae in mice, with the help of natural antibodies (nAbs) and complement system. The spleen slowly but substantially cleared encapsulated pneumococci from the bloodstream in the early phase of blood infection, especially the serotypes that resist to liver filtration. Among splenic macrophage subpopulations, only the lack of RP macrophages led to the complete loss of the splenic immunity. Intravital microscopy detected direct capture and phagocytic killing of circulating pneumococci by RP macrophages in the absence of neutrophils and inflammatory monocytes. Likewise, plasma nAbs targeting pneumococcal cell wall phosphocholine and complement protein C3 were essential for RP macrophage-mediated immune clearance. Our findings have thus uncovered the long-sought immune pathway against invasive pneumococcal infections in the spleen. Short summaryThe spleen plays a crucial role in defending against invasive infections caused by Streptococcus pneumoniae (pneumococcus) and other encapsulated bacteria in humans, but the mechanisms underlying this organ-specific immunity remain largely elusive. This study has revealed that the spleen eliminates pneumococci through a coordinated interplay among red pulp macrophages, serum nAbs targeting phosphocholine and the complement system.

microbiology↗

bioRxiv2024

Biochemical and structural insights into a 5' to 3' RNA ligase reveal a potential role in tRNA ligation

ATP-grasp superfamily enzymes contain a hand-like ATP-binding fold and catalyze a variety of reactions using a similar catalytic mechanism. More than 30 protein families are categorized in this superfamily, and they are involved in a plethora of cellular processes and human diseases. Here we identify C12orf29 as an atypical ATP-grasp enzyme that ligates RNA. Human C12orf29 and its homologs auto-adenylate on an active site Lys residue as part of a reaction intermediate that specifically ligates RNA halves containing a 5-phosphate and a 3-hydroxyl. C12orf29 binds tRNA in cells and can ligate tRNA within the anticodon loop in vitro. Genetic depletion of c12orf29 in female mice alters global tRNA levels in brain. Furthermore, crystal structures of a C12orf29 homolog from Yasminevirus bound to nucleotides reveal a minimal and atypical RNA ligase fold with a unique active site architecture that participates in catalysis. Collectively, our results identify C12orf29 as an RNA ligase and suggest its involvement in tRNA biology. Significance StatementATP-grasp enzymes share an atypical ATP-binding fold and catalyze a diverse set of reactions involved in many essential cellular processes. We identified C12orf29 as an atypical ATP-grasp enzyme. Our biochemical and structural characterizations reveal this enzyme to be a 5 to 3 RNA ligase, structurally and functionally similar to the phage T4 RNA ligase. C12orf29 can ligate tRNAs in vitro and C12orf29 knockout female mice have altered tRNA levels in brain. We also report structures of C12orf29, which have revealed critical insights into the mode of ATP binding and catalysis. Our work suggests that C12orf29 may be a new player in the regulation of tRNAs.

biochemistry↗

bioRxiv2024

Allele-specific targeting of mutant TOR1A by the compact CRISPR/NmCas9 system in DYT1 dystonia with high fidelity

DYT1 is an autosomal dominant form of isolated dystonia, which is basically caused by an in-frame 3-bp GAG deletion in the TOR1A gene, leading to loss of a single glutamic acid residue ({Delta}E) at the C-terminus. TOR1A has been strongly implicated in various biological processes, such as protein quality control and regulation of ER stress. Many of these functions involve as protein multimers between TOR1A and its partners, whereas the {Delta}E mutant leads to destabilization of their binding, thereby reducing ATPase activation. Despite controversy over its functional model, the dominant-negative nature of TOR1A{Delta}E has been demonstrated in a number of ways. Therefore, it is promising to develop an allele-specific intervention strategy that specifically silences the pathogenic TOR1A allele while preserving the wild-type allele to perform its normal function. In this study, we systematically evaluated the allele-specific targeting of TOR1A{Delta}E using over 20 Cas endonucleases. We found that NmCas9, one of the compact Cas endonucleases yet with high-fidelity, selectively targeted the TOR1A{Delta}E allele, with a 3-nt deletion located in the spacer region of sgRNAs. The discriminatory Nm-sgRNAs were verified both exogenously and endogenously that showed high specificity in disrupting the TOR1A{Delta}E allele but not the wild-type one. Functionally, this strategy efficiently ameliorated the ubiquitin accumulation in DYT1 fibroblasts. Overall, our study demonstrates that the allele-specific targeting of mutant TOR1A with NmCas9 is a promising alternative approach for the treatment of DYT1.

molecular biology↗

bioRxiv2024

scCaT: an explainable capsulating architecture for sepsis diagnosis transferring from single-cell RNA sequencing

Sepsis is a life-threatening condition characterized by an exaggerated immune response to pathogens, leading to organ damage and high mortality rates in the intensive care unit. Although deep learning has achieved impressive performance on prediction and classification tasks in medicine, it requires large amounts of data and lacks explainability, which hinder its application to sepsis diagnosis. We introduce a deep learning framework, called scCaT, which blends the capsulating architecture with Transformer to develop a sepsis diagnostic model using single-cell RNA sequencing data and transfers it to bulk RNA data. The capsulating architecture effectively groups genes into capsules based on biological functions, which provides explainability in encoding gene expressions. The Transformer serves as a decoder to classify sepsis patients and controls. Our model achieves high accuracy with an AUROC of 0.93 on the single-cell test set and an average AUROC of 0.98 on seven bulk RNA cohorts. Additionally, the capsules can recognize different cell types and distinguish sepsis from control samples based on their biological pathways. This study presents a novel approach for learning gene modules and transferring the model to other data types, offering potential benefits in diagnosing rare diseases with limited subjects. Author summaryDeep learning models used in disease diagnosis usually suffer from insufficient data for training and the lack of explainability, especially in rare diseases. These shortages hinder their application to sepsis diagnosis. Here we propose a diagnostic framework name scCaT(https://github.com/Kimxbzheng/CaT), which transfers knowledge learned from single-cell RNA-seq, for diseases with insufficient bulk data. The framework uses capsulating architecture to group genes into capsules and provide explainability to the deep learning model for sepsis diagnosis. ScCaT achieves robust and outstanding performance for sepsis diagnosis in both scRNA-seq and bulk RNA datasets. This architecture offers potential approaches in diagnosing rare diseases with limited subjects with explainability.

bioinformatics↗

bioRxiv2024

Antibody-mediated cellular responses are dysregulated in Multisystem Inflammatory Syndrome in Children (MIS-C)

Multisystem Inflammatory Syndrome in Children (MIS-C) is a severe complication of SARS-CoV-2 infection characterized by multi-organ involvement and inflammation. Testing of cellular function ex vivo to understand the aberrant immune response in MIS-C is limited. Despite strong antibody production in MIS-C, SARS-CoV-2 nucleic acid testing can remain positive for 4-6 weeks after infection. Therefore, we hypothesized that dysfunctional cell-mediated antibody responses downstream of antibody production may be responsible for delayed clearance of viral products in MIS-C. In MIS-C, monocytes were hyperfunctional for phagocytosis and cytokine production, while natural killer (NK) cells were hypofunctional for both killing and cytokine production. The decreased NK cell cytotoxicity correlated with an NK exhaustion marker signature and systemic IL-6 levels. Potentially providing a therapeutic option, cellular engagers of CD16 and SARS-CoV-2 proteins were found to rescue NK cell function in vitro. Together, our results reveal dysregulation in antibody-mediated cellular responses unique to MIS-C that likely contribute to the immune pathology of this disease. SummaryMIS-C is a severe complication of SARS-CoV-2 infection characterized by multi-organ involvement and inflammation. Limited studies tested cellular function ex vivo to understand the aberrant immune response in MIS-C. We found dysregulation in antibody-mediated cellular responses unique to MIS-C that likely contribute to the immune pathology of this disease O_FIG O_LINKSMALLFIG WIDTH=138 HEIGHT=200 SRC="FIGDIR/small/589585v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@16d9e0dorg.highwire.dtl.DTLVardef@1a37693org.highwire.dtl.DTLVardef@bdb0cforg.highwire.dtl.DTLVardef@1a32604_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO C_FIG

immunology↗

bioRxiv2024

Lipid Nanoparticle-Associated Inflammation is Triggered by Sensing of Endosomal Damage: Engineering Endosomal Escape without Side Effects

Lipid nanoparticles (LNPs) have emerged as the dominant platform for RNA delivery, based on their success in the COVID-19 vaccines and late-stage clinical studies in other indications. However, we and others have shown that LNPs induce severe inflammation, and massively aggravate pre-existing inflammation. Here, using structure-function screening of lipids and analyses of signaling pathways, we elucidate the mechanisms of LNP-associated inflammation and demonstrate solutions. We show that LNPs hallmark feature, endosomal escape, which is necessary for RNA expression, also directly triggers inflammation by causing endosomal membrane damage. Large, irreparable, endosomal holes are recognized by cytosolic proteins called galectins, which bind to sugars on the inner endosomal membrane and then regulate downstream inflammation. We find that inhibition of galectins abrogates LNP-associated inflammation, both in vitro and in vivo. We show that rapidly biodegradable ionizable lipids can preferentially create endosomal holes that are smaller in size and reparable by the endosomal sorting complex required for transport (ESCRT) pathway. Ionizable lipids producing such ESCRT-recruiting endosomal holes can produce high expression from cargo mRNA with minimal inflammation. Finally, we show that both routes to non-inflammatory LNPs, either galectin inhibition or ESCRT-recruiting ionizable lipids, are compatible with therapeutic mRNAs that ameliorate inflammation in disease models. LNPs without galectin inhibition or biodegradable ionizable lipids lead to severe exacerbation of inflammation in these models. In summary, endosomal escape induces endosomal membrane damage that can lead to inflammation. However, the inflammation can be controlled by inhibiting galectins (large hole detectors) or by using biodegradable lipids, which create smaller holes that are reparable by the ESCRT pathway. These strategies should lead to generally safer LNPs that can be used to treat inflammatory diseases.

bioengineering↗

bioRxiv2024

Comprehensive evaluation and prediction of editing outcomes for near-PAMless adenine and cytosine base editors

Base editors enable the direct conversion of target bases without inducing double-strand breaks, showing great potential for disease modeling and gene therapy. Yet, their applicability has been constrained by the necessity for specific protospacer adjacent motif (PAM). We generated four versions of near-PAMless base editors and systematically evaluated their editing patterns and efficiencies using an sgRNA-target library of 45,747 sequences. Near-PAMless base editors significantly expanded the targeting scope, with both PAM and target flanking sequences as determinants for editing outcomes. We developed BEguider, a deep learning model to accurately predict editing results for near-PAMless base editors. We also provided experimentally measured editing outcomes of 20,541 ClinVar sites, demonstrating that variants previously inaccessible by NGG PAM base editors can now be precisely generated or corrected. We have made our predictive tool and data available online to facilitate development and application of near-PAMless base editors in both research and clinical settings.

bioinformatics↗

bioRxiv2024

Prominent involvement of acetylcholine in shaping stable olfactory representation across the Drosophila brain

Despite the vital role of neuromodulation in the neural system, the specific spatiotemporal dynamics of neuromodulators and their interactions with neuronal activities in vivo are still unclear, hampering our understanding of their information representation and functional contributions systemically. To address this problem, we employed two-photon synthetic aperture microscopy (2pSAM) to record long-term neuronal and neuromodulatory olfactory responses across the Drosophila brain at high speed. Our results revealed distinct response properties, global information propagation, functional connectivity, and odor identity representation among neuronal, cholinergic, and serotoninergic dynamics across multiple brain regions. We discovered the compensation between neuronal activity and cholinergic dynamics, both in the odor identity representation across the brain and the functional connectivity network structures of specific brain regions. Moreover, employing low-dimensional manifold and functional connectivity network analyses, we characterized the stable representation of cholinergic dynamics over a long term. Collectively, our unbiased and comprehensive investigation unveiled the prominent involvement of acetylcholine (ACh) in shaping olfactory representation across the brain, underscoring the inadequacy of solely considering neuronal activities when examining information representation of the brain.

neuroscience↗

bioRxiv2024

Unveiling Frequency-Specific Microstate Correlates of Anxiety and Depression Symptoms

Electroencephalography (EEG) microstates are canonical voltage topographies that reflect the temporal dynamics of resting-state brain networks on a millisecond time scale. Changes in microstate parameters have been described in patients with psychiatric disorders, indicating their potential as clinical biomarkers with broadband EEG signals (e.g., 1-30 Hz). Considering the distinct information provided by specific frequency bands, we hypothesized that microstates in decomposed frequency band could provide a more detailed depiction of the underlying psychological mechanism. In this study, with a large open access resting-state dataset (n = 203), we examined the properties of frequency-specific microstates and their relationship with emotional disorders. We conducted clustering on EEG topographies in decomposed frequency band (delta, theta, alpha and beta), and determined the number of clusters with a meta-criterion. Microstate parameters, including global explained variance (GEV), duration, coverage, occurrence and transition probability, were calculated for eyes-open and eyes-closed states, respectively. Their predictive power for the scores of depression and anxiety symptoms were identified by correlation and regression analysis. Distinct microstate patterns were observed across different frequency bands. Microstate parameters in the alpha band held the best predictive power for emotional symptoms. Microstates B (GEV, coverage) and parieto-central maximum microstate C (coverage, occurrence, transitions from B to C) in the alpha band exhibited significant correlations with depression and anxiety, respectively. Microstate parameters of the alpha band achieved predictive R-square of 0.100 for anxiety scores, which is much higher than those of broadband (R-square = -0.026, p < .01). These results suggested the value of frequency-specific microstates in predicting emotional symptoms.

neuroscience↗

bioRxiv2024

Self-organization of vascularized skeletal muscle from bovine embryonic stem cells

Cultured beef holds promising potential as an alternative to traditional meat options. While adult stem cells are commonly used as the cell source for cultured beef, their proliferation and differentiation capacities are limited. To produce cultured beef steaks, current manufacturing plans often require the separate preparation of multiple cell types and intricate engineering for assembling them into structured tissues. In this study, we propose and report the co-induction of skeletal muscle, neuronal, and endothelial cells from bovine embryonic stem cells (ESCs) and the self-organization of tissue structures in 2- and 3-dimensional cultures. Bovine myocytes were induced in a stepwise manner through the induction of presomitic mesoderm (PSM) from bovine ESCs. Muscle fibers with sarcomeres appeared within 15 days, displaying calcium oscillations responsive to inputs from co-induced bovine spinal neurons. Bovine endothelial cells were also co-induced via PSM, forming uniform vessel networks inside tissues. Our serum-free, rapid co-induction protocols represent a milestone toward self-organizing beef steaks with integrated vasculature and innervation.

bioengineering↗

bioRxiv2024

Transcription factor EB (TFEB) interaction with RagC is disrupted during Enterovirus D68 Infection

Enterovirus D68 (EV-D68) is a picornavirus associated with severe respiratory illness and a paralytic disease called acute flaccid myelitis in infants. Currently, no protective vaccines or antivirals are available to combat this virus. Like other enteroviruses, EV-D68 uses components of the cellular autophagy pathway to rewire membranes for its replication. Here, we show that transcription factor EB (TFEB), the master transcriptional regulator of autophagy and lysosomal biogenesis, is essential for EV-D68 infection. Knockdown of TFEB attenuated EV-D68 genomic RNA replication but did not impact viral binding or entry into host cells. The 3C protease of EV-D68 cleaves TFEB at the N-terminus immediately post-peak viral RNA replication, disrupting TFEB-RagC interaction and restricting TFEB transport to the surface of the lysosome. Despite this, TFEB remained mostly cytosolic during EV-D68 infection. Overexpression of a TFEB mutant construct lacking the RagC binding domain, but not the wild-type construct, blocks autophagy and increases EV-D68 nonlytic release in H1HeLa cells, but not in autophagy defective ATG7 KO H1HeLa cells. Our results identify TFEB as a vital host factor regulating multiple stages of the EV-D68 lifecycle and suggest that TFEB could be a promising target for antiviral development against EV-D68. ImportanceEnteroviruses are among the most significant causes of human disease. Some enteroviruses are responsible for severe paralytic diseases such as poliomyelitis or acute flaccid myelitis (AFM). The latter disease is associated with multiple non-polio enterovirus species, including Enterovirus D68 (EV-D68), Enterovirus 71 (EV-71), and coxsackievirus B3 (CVB3). Here we demonstrate that EV-D68 interacts with a host transcription factor, TFEB, to promote vRNA replication and regulate egress of virions from cells. TFEB was previously implicated in viral egress of CVB3, and the viral protease 3C cleaves TFEB during infection. Here we show EV-D68 3C protease also cleaves TFEB after the peak of vRNA replication. This cleavage disrupts TFEB interaction with the host protein RagC, which changes the localization and regulation of TFEB. TFEB lacking a RagC-binding domain inhibits autophagic flux and promotes virus egress. These mechanistic insights highlight how common host factors affect closely related, medically-important viruses differently.

microbiology↗

bioRxiv2024

Bioorthogonal labeling and enrichment of histone monoaminylation reveal its accumulation and regulatory function in cancer cell chromatin

Histone monoaminylation (i.e., serotonylation and dopaminylation) is an emerging category of epigenetic mark occurring on the fifth glutamine (Q5) residue of H3 N-terminal tail, which plays significant roles in gene transcription. Current analysis of histone monoaminylation is mainly based on site-specific antibodies and mass spectrometry, which either lacks high resolution or is time-consuming. In this study, we report the development of chemical probes for bioorthogonal labeling and enrichment of histone serotonylation and dopaminylation. These probes were successfully applied for the monoaminylation analysis of in vitro biochemical assays, cells, and tissue samples. The enrichment of monoaminylated histones by the probes further confirmed the crosstalk between H3Q5 monoaminylation and H3K4 methylation. Finally, combining the ex vivo and in vitro analyses based on the developed probes, we have shown that both histone serotonylation and dopaminylation are highly enriched in tumor tissues that overexpress transglutaminase 2 (TGM2) and regulate the three-dimensional architecture of cellular chromatin. TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=154 SRC="FIGDIR/small/586010v3_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@1bee3f7org.highwire.dtl.DTLVardef@1687013org.highwire.dtl.DTLVardef@1960bd0org.highwire.dtl.DTLVardef@1e19a04_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

GeneSurv: Multi-Gene Cancer Survival Analysis Tool

SummaryTraditional cancer survival analysis tools often restrict their analysis to single genes, thereby limiting their analytical scope. GeneSurv, a novel Web-Based Multi-Gene Cancer Survival Analysis Tool, addresses this limitation by enabling multi-gene analyses that correlates the expression of multiple genes, without restriction on their number, in various combinations, with patient survival outcomes. GeneSurv offers dynamic functionalities and an intuitive interface for flexible and precise adjustments of gene expression thresholds. Among its demonstrated applications, GeneSurv identified a significant association between high expression of CCND1 and CDK4 with poor breast cancer prognosis, and related the combined expression of five genes to patient survival, showcasing its capacity to unravel the complexities of genetic interactions and their impact on patient outcomes. ConclusionAvailable with user-friendly tutorials at https://can-sat.erc.monash.edu/, GeneSurv is an invaluable addition to the existing suite of bioinformatic tools, significantly enhancing the investigation of cancer prognosis.

bioinformatics↗

bioRxiv2024

Evolutionary trajectory of TRPM2 channel activation by adenosine diphosphate ribose and calcium

Ion channel activation upon ligand gating triggers a myriad of biological events and, therefore, evolution of ligand gating mechanism is of fundamental importance. TRPM2, a typical ancient ion channel, is activated by adenosine diphosphate ribose (ADPR) and calcium and its activation has evolved from a simple mode in invertebrates to a more complex one in vertebrates, but the evolutionary process is still unknown. Molecular evolutionary analysis of TRPM2s from more than 280 different animal species has revealed that, the C-terminal NUDT9-H domain has evolved from an enzyme to a ligand binding site for activation, while the N-terminal MHR domain maintains a conserved ligand binding site. Calcium gating pattern has also evolved, from one Ca2+-binding site as in sea anemones to three sites as in human. Importantly, we identified a new group represented by olTRPM2, which has a novel gating mode and fills the missing link of the channel gating evolution. We conclude that the TRPM2 ligand binding or activation mode evolved through at least three identifiable stages in the past billion years from simple to complicated and coordinated. Such findings benefit the evolutionary investigations of other channels and proteins.

evolutionary biology↗

bioRxiv2024

A brain-to-text framework of decoding natural tonal sentences

Speech brain-computer interfaces (BCIs) directly translate brain activity into speech sound and text, yet decoding tonal languages like Mandarin Chinese poses a significant, unexplored challenge. Despite successful cases in non-tonal languages, the complexities of Mandarin, with its distinct syllabic structures and pivotal lexical information conveyed through tonal nuances, present challenges in BCI decoding. Here we designed a brain-to-text framework to decode Mandarin tonal sentences from invasive neural recordings. Our modular approach dissects speech onset, base syllables, and lexical tones, integrating them with contextual information through Bayesian likelihood and the Viterbi decoder. The results demonstrate accurate tone and syllable decoding under variances in continuous naturalistic speech production, surpassing previous intracranial Mandarin tonal syllable decoders in decoding accuracy. We also verified the robustness of our decoding framework and showed that the model hyperparameters can be generalized across participants of varied gender, age, education backgrounds, pronunciation behaviors, and coverage of electrodes. Our pilot study shed lights on the feasibility of more generalizable brain-to-text decoding of natural tonal sentences from patients with high heterogeneities.

neuroscience↗

bioRxiv2024

A high resolution model of the grapevine leaf morphospace predicts synthetic leaves

O_LIGrapevine leaves are a model morphometric system. Sampling over ten thousand leaves using dozens of landmarks, the genetic, developmental, and environmental basis of leaf shape has been studied and a morphospace for the genus Vitis predicted. Yet, these representations of leaf shape fail to capture the exquisite features of leaves at high resolution. C_LIO_LIWe measure the shapes of 139 grapevine leaves using 1672 pseudo-landmarks derived from 90 homologous landmarks with Procrustean approaches. From hand traces of the vasculature and blade, we have derived a method to automatically detect landmarks and place pseudo-landmarks that results in a high-resolution representation of grapevine leaf shape. Using polynomial models, we create continuous representations of leaf development in 10 Vitis spp. C_LIO_LIWe visualize a high-resolution morphospace in which genetic and developmental sources of leaf shape variance are orthogonal to each other. Using classifiers, V. vinifera, Vitis spp., rootstock and dissected leaf varieties as well as developmental stages are accurately predicted. Theoretical eigenleaf representations sampled from across the morphospace that we call synthetic leaves can be classified using models. C_LIO_LIBy predicting a high-resolution morphospace and delimiting the boundaries of leaf shapes that can plausibly be produced within the genus Vitis, we can sample synthetic leaves with realistic qualities. From an ampelographic perspective, larger numbers of leaves sampled at lower resolution can be projected onto this high-resolution space; or, synthetic leaves can be used to increase the robustness and accuracy of machine learning classifiers. C_LI Societal Impact StatementGrapevine leaves are emblematic of the strong visual associations people make with plants. At a glance, leaf shape is immediately recognizable, and it is because of this reason it is used to distinguish grape varieties. In an era of computationally-enabled, machine learning-derived representations of reality, we can revisit how we view and use the shapes and forms that plants display to understand our relationship with them. Using computational approaches combined with time-honored methods, we can predict theoretical leaves that are possible to understand the genetics, development, and environmental responses of plants in new ways.

plant biology↗

bioRxiv2024

Robust Methods For Quantifying Neuronal Morphology And Molecular Signaling Reveal That Psychedelics Do Not Induce Neuroplasticity

Induction of neuroplasticity has become the dominant explanatory framework for the rapid and sustained therapeutic effects of classic psychedelics. Within this broad concept, examination of morphological neuronal plasticity, such as dendritic arbor growth, is widely used to assess the neuroplasticity effects of classic and novel psychedelics. At the molecular level, it has been reported that serotonergic psychedelic compounds mediate dendritogenesis via the master molecular regulator of plasticity, TrkB, either directly via BDNF/TrkB signaling potentiation or indirectly through 5-HT2A receptor. To examine these hypotheses in detail, we developed a robust multimodal screening platform for unbiased, semi-automated quantification of cellular morphology and multiplex molecular signaling in the same cortical neurons. We found that in widely used primary neuronal cultures psychedelics do not directly modulate TrkB receptor or BDNF-TrkB signaling. We also found 5HT2a receptor gene expression and functional receptor levels are low, and psychedelics do not induce morphological growth, in contrast to significant dendritogenesis elicited by BDNF. Our results challenge recently published results in the field and indicate a need for rigorous experimental methods to study morphological manifestations of neuroplasticity effects induced by clinically used and experimental therapeutics.

neuroscience↗