Biology subjects

Liu, Y.

Publications and source records attributed to Liu, Y..

At least 1,135 records · Page 63Linked to original sources

bioRxiv2024

Drug resistant pancreatic cancer cells exhibit altered biophysical interactions with stromal fibroblasts in imaging studies of 3D co-culture models

Interactions between tumor and stromal cells are well known to play a prominent roles in progression of pancreatic ductal adenocarcinoma (PDAC). As knowledge of stromal crosstalk in PDAC has evolved, it has become clear that cancer associated fibroblasts can play both tumor promoting and tumor suppressive roles through a combination of paracrine crosstalk and juxtacrine interactions involving direct physical contact. Another major contributor to dismal survival statistics for PDAC is development of resistance to chemotherapy drugs. Though less is known about how the acquisition of chemoresistance impacts upon tumor-stromal crosstalk. Here, we use 3D co-culture geometries to recapitulate juxtacrine interactions between epithelial and stromal cells. In particular, extracellular matrix (ECM) overlay cultures in which stromal cells (pancreatic stellate cells, or normal human fibroblasts) are placed adjacent to PDAC cells (PANC1), result in direct heterotypic cell adhesions accompanied by dramatic fibroblast contractility which leads to highly condensed macroscopic multicellular aggregates as detected using particle image velocimetry (PIV) analysis to quantify cell velocities over the course of time lapse movie sequences. To investigate how drug resistance impacts these juxtacrine interactions we contrast cultures in which PANC1 are substituted with a drug resistant subline (PANC1-OR) previously established in our lab. We find that heterotypic cell-cell interactions are highly suppressed in drug-resistant cells relative to the parental PANC1 cells. To investigate further we conduct RNA-seq and bioinformatics analysis to identify differential gene expression in PANC1 and PANC1-OR, which shows that negative regulation of cell adhesion molecules, consistent with increased epithelial mesenchymal transition (EMT), is also consistent with loss of hetrotypic cell-cell contact necessary for the contractile behavior observed in drug naive cultures. Overall these findings elucidate the role of drug-resistance in inhibiting an avenue of stromal crosstalk which is associated with tumor suppression and also help to establish cell culture conditions useful for further mechanistic investigation.

biophysics↗

bioRxiv2024

Sequence-specific targeting of intrinsically disordered protein regions

Intrinsically disordered proteins and peptides play key roles in biology, but the lack of defined structures and the high variability in sequence and conformational preferences has made targeting such systems challenging. We describe a general approach for designing proteins that bind intrinsically disordered protein regions in diverse extended conformations with side chains fitting into complementary binding pockets. We used the approach to design binders for 39 highly diverse unstructured targets and obtain designs with pM to 100 nM affinities in 34 cases, testing [~]22 designs per target (including polar targets). The designs function in cells and as detection reagents, and are specific for their intended targets in all-by-all binding experiments. Our approach is a major step towards a general solution to the intrinsically disordered protein and peptide recognition problem.

biochemistry↗

bioRxiv2024

SlNAP2 promoted fruit ripening by directly binding the ACS2 promoter and interacting with EIL3

The ripening process of tomato fruit is affected by a variety of environmental factors and genetic regulators. NAC transcription factors (TFs) function in a multitude of biological processes, while the current knowledge on the participation of NAC TFs in the regulatory network of fruit ripening is relatively limited. In this study, we isolated a NAC TFs, NAP2, which acts as a positive transcription activator in tomato fruit ripening. We also observed a notable delay in the ripening process of SlNAP2 silenced and knockout mutant fruit. In particular, ethylene production was obviously inhibited in SlNAP2 mutant fruit. Y1H and DLR assays showed that SlNAP2 directly binds to the promoter of SlACS2 and activates its transcriptional activity. Furthermore, SlNAP2 and SlEIL3 physically interaction was demonstrated by yeast two-hybrid (Y2H), luciferase complementation (LUC), bimolecular fluorescence complementation (BiFC) and coimmunoprecipitation analysis (CoIP) assays. Meanwhile, the pigment content, firmness and the transcript levels of genes associated with carotenoid and chlorophyll metabolism and cell wall metabolism were also potentially affected by the SlNAP2 deletion; however, it has remained unclear whether these genes are also directly regulated by SlNAP2. Therefore, our findings indicate that SlNAP2 directly binds to SlACS2 promoter to activate its expression and promote ethylene generation, which in turn interacts with EIL3 to enhance the function of ethylene in tomato fruit ripening. Collectively, our data contribute to understanding the interaction of NAC TFs and ethylene in tomato fruit ripening, thereby enhancing our knowledge of the ripening regulatory network that governs tomato fruit maturation.

biochemistry↗

bioRxiv2024

Neuronal GPCR NMUR-1 regulates energy homeostasis in response to pathogen infection

A key question in current immunology is how the innate immune system generates high levels of specificity. Our previous study in Caenorhabditis elegans revealed that NMUR-1, a neuronal G protein-coupled receptor homologous to mammalian receptors for the neuropeptide neuromedin U (NMU), regulates distinct innate immune responses to different bacterial pathogens. Here, by using quantitative proteomics and functional assays, we discovered that NMUR-1 regulates F1FO ATP synthase and ATP production in response to pathogen infection, and that such regulation contributes to NMUR-1-mediated specificity of innate immunity. We further demonstrated that ATP biosynthesis and its contribution to defense is neurally controlled by the NMUR-1 ligand CAPA-1 and its expressing neurons ASG. These findings indicate that NMUR-1 neural signaling regulates the specificity of innate immunity by controlling energy homeostasis as part of defense against pathogens. Our study provides mechanistic insights into the emerging roles of NMU signaling in immunity across animal phyla.

immunology↗

bioRxiv2024

Moderate Cold Stress Enhance Drought Resistance through CCA1 via -an ABA- independent Pathway

In nature, plants frequently encounter concurrent stresses, particularly the simultaneous occurrence of cold and drought stress poses a challenge to plants in middle and high latitudes. However, the molecular mechanisms underlying the plants response to this double-stress scenario remain unclear. Although some responses suggest that drought stress can improve cold resistance in plants, through ABA signaling pathways. In our study, we discovered that moderate low temperature treatment significantly enhanced Arabidopsis drought tolerance. Low temperature rapidly triggers the transcription factor CCA1, a prototypical response to cold stress, which inturn directly regulates the expression of OST1 and P5CS1 by binding to their promoters. This leads to the premature closure of stomata and accumulation of proline through a non-ABA-dependent pathway even before plants experience drought stress, ultimately improving plant resistance against drought and cold. Moreover, this mechanism is conserved across plant species, and the synergistic resistance mechanism enables perennial plants to survive winter conditions and annual plants to withstand multi-stresses.

cell biology↗

bioRxiv2024

Ventral Morphology and Ecological Implications of Cindarella eucalla (Artiopoda, Xandarellida) from Chengjiang Biota, China

Artiopoda, an early arthropod group, displays post-antennal appendages resembling trilobite limbs, but relationships with other ealy arthropods remain enigmatic. Limited studies and morphological details hinder the understanding of internal relationships within Artiopoda. Recently, exceptionally well preserved arthropod fossils from the Chengjiang Biota were studied using X-ray computed tomography, revealing detailed morphologies. In this study, Cindarella eucalla, a xandarellid from the Chengjiang Biota, was re-investigated using X-ray computed tomography and fluorescent microscopy to reconstruct its morphology and understand its phylogeny and ecology. This study successfully reconstructed a three-dimensional model of Cindarella eucalla, revealing features, such as spindle-shaped trunk tergites with the anterior six covered by the head shield and axial spines extending from the last four, natant hypostome, four post-antennal cephalic appendage pairs, dorsoventral mismatch existed between trunk tergites and limb pairs. This research suggests that Cindarella eucalla could escape in a very short time when it encounters an enemy, and it probably lived in muddy environments with ample light. Phylogenetic analysis indicates that Xandarellids may have close relationship with concililiterga or a clade composed of Nektaspida + (Conciliterga + (Phytophilaspis pergamena + Trilobita)).

evolutionary biology↗

bioRxiv2024

Septins function in exocytosis via physical interactions with the exocyst complex in fission yeast cytokinesis

Septins can function as scaffolds for protein recruitment, membrane-bound diffusion barriers, or membrane curvature sensors. Septins are important for cytokinesis, but their exact roles are still obscure. In fission yeast, four septins (Spn1 to Spn4) accumulate at the rim of the division plane as rings. The octameric exocyst complex, which tethers exocytic vesicles to the plasma membrane, exhibits a similar localization and is essential for plasma membrane deposition during cytokinesis. Without septins, the exocyst spreads across the division plane but absent from the rim during septum formation. These results suggest that septins and the exocyst physically interact for proper localization and function. Indeed, we predicted six pairs of interactions between septin and exocyst subunits by AlphaFold, most of them are confirmed by co-immunoprecipitation and yeast two-hybrid assays. Exocyst mislocalization results in mistargeting of secretory vesicles and their cargos, which leads to cell-separation delay in septin mutants. Our results indicate that septins guide the targeting of exocyst complex on the plasma membrane for vesicle tethering during cytokinesis through physical interactions.

cell biology↗

bioRxiv2024

Differential Anti-Inflammatory Effects of Electrostimulation in a Standardized Setting

The therapeutic usage of physical stimuli is framed in a highly heterogeneous research area, with variable levels of maturity and of translatability into clinical application. In particular, electrostimulation is deeply studied for its application on the autonomous nervous system, but less is known about the anti-inflammatory effects of such stimuli beyond the inflammatory reflex. Further, reproducibility and meta-analyses on existing results are extremely challenging, owing to the limited rationale on dosage and experimental standardization. In this work we propose a series of controlled experiments on the effects of electrical stimuli (in direct and alternate current) delivered on a standardized 3D bioconstruct constituted by fibroblasts and keratinocytes in a collagen matrix. Transcriptomics backed by metabolomics at selected time points allow to obtain a first systematic overview of the biological functions at stake, highlighting the differential anti-inflammatory potential of such approaches, with promising results for 5V direct current stimuli. We hope that our results will trigger an interest and a facilitation in the study of the anti-inflammatory effects of physical stimuli, highlighting not only the potential but also the limitations of such approaches, offering, ultimately, solid evidence for future translation into the clinic.

systems biology↗

bioRxiv2024

RBM10 loss induces aberrant splicing of cytoskeletal and extracellular matrix mRNAs and promotes metastatic fitness.

RBM10 modulates transcriptome-wide cassette exon splicing. Loss-of-function RBM10 mutations are enriched in thyroid cancers with distant metastases. Analysis of transcriptomes and genes mis-spliced by RBM10 loss showed pro-migratory and RHO/RAC signaling signatures. RBM10 loss increases cell velocity. Cytoskeletal and ECM transcripts subject to exon-inclusion events included vinculin (VCL), tenascin C (TNC) and CD44. Knockdown of the VCL exon inclusion transcript in RBM10-null cells reduced cell velocity, whereas knockdown of TNC and CD44 exon-inclusion isoforms reduced invasiveness. RAC1-GTP levels were increased in RBM10-null cells. Mouse HrasG12V/Rbm1OKO thyrocytes develop metastases that are reversed by RBM10 or by combined knockdown of VCL, CD44 and TNC inclusion isoforms. Thus, RBM10 loss generates exon inclusions in transcripts regulating ECM-cytoskeletal interactions, leading to RAC1 activation and metastatic competency. Moreover, a CRISPR-Cas9 screen for synthetic lethality with RBM10 loss identified NFkB effectors as central to viability, providing a therapeutic target for these lethal thyroid cancers. SUMMARYRNA splicing factor mutations are common in cancer but connecting phenotypes to specific misspliced genes has been challenging. We show that RBM10 loss leads to exon inclusions of transcripts regulating ECM-cytoskeletal interactions and RAC1-GTP activation, sufficient to promote metastatic fitness.

cancer biology↗

bioRxiv2024

Clathrin-associated carriers enable recycling through a kiss-and-run mechanism

Endocytosis and recycling control the uptake and retrieval of various materials, including membrane proteins and lipids, in all eukaryotic cells. These processes are crucial for cell growth, organization, function, and environmental communication. However, the mechanisms underlying efficient, fast endocytic recycling remain poorly understood. Here, by utilizing a biosensor and imaged-based screening, we uncover a novel recycling mechanism that couples endocytosis and fast recycling, which we name the clathrin-associated fast endosomal recycling pathway (CARP). Clathrin-associated tubulovesicular carriers containing clathrin, AP1, Arf1, Rab1, and Rab11, while lacking the multimeric retrieval complexes, are generated at subdomains of early endosomes, and then transported along actin to cell surfaces. Unexpectedly, the clathrin-associated recycling carriers undergo partial fusion with the plasma membrane. Subsequently, they are released from the membrane by dynamin and reenter cells. Multiple receptors utilize and modulate CARP for fast recycling following endocytosis. Thus, CARP represents a novel endocytic recycling mechanism with kiss-and-run membrane fusion.

cell biology↗

bioRxiv2024

Droplet-AI-empowered high-throughput screening of cell-free gene expression

Cell-free gene expression (CFE) systems enable transcription and translation using crude cellular extracts, offering a versatile platform for synthetic biology by eliminating the need to maintain living cells. This allows direct manipulation of molecular components and the focused synthesis of specific products. However, the optimization of CFE systems is constrained by cumbersome composition, high costs, and limited yields due to numerous additional components required to maintain biocatalytic efficiency. While optimizing such complicated systems is daunting for existing high-throughput screening means, we introduce DropAI, a droplet-based, AI-driven screening strategy designed to optimize CFE systems with high throughput and economic efficiency. DropAI employs microfluidics to generate picoliter reactors and utilizes a fluorescent color-based coding-decoding system to address and screen a vast array of additive combinations. The in-droplet screening is complemented by in silico optimization, where experimental results train a machine-learning model to estimate the contribution of the components and predict high-yield combinations, which are then validated in vitro. Applying DropAI to an Escherichia coli-based CFE system, we simplified a set of 12 additives to only 3 essential components. Through further optimization, we achieved a 2.1-fold cost reduction and a 1.9-fold increase in yield for the expression of superfolder green fluorescent protein (sfGFP). This optimized formulation was further validated across 12 different proteins. Notably, the established E. coli model is successfully adapted to a Bacillus subtilis-based system through transfer learning, leading to doubled yield through prediction. DropAI thus offers a generalizable and scalable method for optimizing CFE systems, enhancing their potential for biochemical engineering and biomanufacturing applications.

bioengineering↗

bioRxiv2024

Cerebellar output neurons impair non-motor behaviors by altering development of extracerebellar connectivity

The capacity of the brain to compensate for insults during development depends on the type of cell loss, whereas the consequences of genetic mutations in the same neurons are difficult to predict. We reveal powerful compensation from outside the cerebellum when the excitatory cerebellar output neurons are ablated embryonically and demonstrate that the minimum requirement for these neurons is for motor coordination and not learning and social behaviors. In contrast, loss of the homeobox transcription factors Engrailed1/2 (EN1/2) in the cerebellar excitatory lineage leads to additional deficits in adult learning and spatial working memory, despite half of the excitatory output neurons being intact. Diffusion MRI indicates increased thalamo-cortico-striatal connectivity in En1/2 mutants, showing that the remaining excitatory neurons lacking En1/2 exert adverse effects on extracerebellar circuits regulating motor learning and select non-motor behaviors. Thus, an absence of cerebellar output neurons is less disruptive than having cerebellar genetic mutations.

neuroscience↗

bioRxiv2024

A chromosome-level genome assembly of Dracaena cambodiana and comparative genomics analysis highlights the distinct biological features of two resource species of dragon's blood

This study reports a chromosome-level genome for Dracaena cambodiana, one of two typical dracaena species in China. This work will help to deepen the understanding of the dracaena species and the conservation and development of plant resources. The final assembly consisted of 54 scaffolds, spanning 1.08 Gb, with a scaffold N50 size of 52.29 Mb, encoded 36860 predicted protein-coding genes. A total of 1,064,810,157 bp of genome sequences were located on 20 chromosomes (2n = 40), accounting for 98.46%. We investigate the possible mechanisms of the longevity of dracaena, the longest-lived plant in the world, which involve DNA repair and post-translational modification. We also performed comparative genomic analysis of the previously assembled genome of Dracaena cochinchinesis with this genome, and found that the two involved interaction of plant-pathogen interaction and ubiquitin mediated proteolysis, which may reveal why Dracaena has environmental adaptability and longevity characteristics.

genomics↗

bioRxiv2024

Basal Cambrian soft-bodied segmented bilaterians preserved as microbial pseudomorphs

Before Cambrian Stage 3, unambiguous body fossils of segmented bilaterians were rare, severely hampering our understanding of the early history of such important animals. Here we report a variety of microfossils with quintessential features such as paired appendages, dorsoventral and anteroposterior differentiations from the basal Cambrian Fortunian of South China, representing the earliest known three-dimensional body fossils of segmented bilaterians. These fossils were all microbial pseudomorphs built up by secondarily phosphatized bacteria aggregations, testifying microbial pseudomorph could serve as a novel and important pathway to preserve tiny, fragile bilaterian progenitors. This finding unveils a diversified segmented bilaterian world at the very beginning of Cambrian and would arouse a more comprehensive perspective on the early evolution of bilaterian body plans.

paleontology↗

bioRxiv2024

Alpine lakes harbor diverse, endemic and structurally unique RNA viruses

Alpine lakes, characterized by isolation, low temperatures, oligotrophic conditions, and intense ultraviolet radiation, remain a poorly explored ecosystem for RNA viruses. Here, we present the first comprehensive metatranscriptomic study of RNA viruses in Lake Nam Co, a high-altitude alkaline saline lake on the Tibetan Plateau. Using a combination of sequence- and structure-based homology searches, we identified 742 RNA virus species, including 383 novel genus-level groups and 84 novel family-level groups exclusively found in Lake Nam Co. These findings significantly expand the known diversity of the Orthornavirae, uncovering evolutionary adaptations such as permutated RNA-dependent RNA polymerase (RdRP) motifs and distinct RNA secondary structures. Notably, 14 previously unknown RNA virus families potentially infecting prokaryotes were predicted, broadening the known host range of RNA viruses and questioning the traditional assumption that RNA viruses predominantly target eukaryotes. The presence of auxiliary metabolic genes (AMGs) in viral genomes suggested that RNA viruses (families f.0102 and Nam-Co_family_51) exploit host energy production mechanisms in energy-limited alpine lakes. Low nucleotide diversity, SNP frequencies, and pN/pS ratios indicate strong purifying selection in Nam Co viral populations. Our findings offer insights into RNA virus evolution and ecology, highlighting the importance of extreme environments in uncovering hidden viral diversity, and further shed light into their potential ecological implications, particularly in the context of climate change. Significance StatementThis study unveils the hidden diversity and complexity of RNA viruses in the high-altitude ecosystem of Lake Nam Co, significantly expanding the known RNA virome. The discovery of novel viral clades, expanded potential host ranges, and unique evolutionary adaptations emphasizes the importance of exploring extreme environments to uncover viral diversity and evolutionary pathways. Our findings offer critical insights into viral evolution, host-virus interactions, and the ecological roles of RNA viruses, particularly in the context of climate change and environmental resilience.

microbiology↗

bioRxiv2024

Large-scale genome analyses provide insights into Hymenoptera evolution

The order Hymenoptera includes a large number of species with diverse lifestyles and is known for its significant contributions to natural ecosystems. To better understand the evolution of this diverse order, we performed large-scale comparative genomics on 131 species from 13 superfamilies, covering most representative groups. We used these genomes to reveal an overall pattern of genomic change in terms of gene content and evolutionary rate throughout hymenopteran history. We identified genes that possibly contributed to the evolution of several key innovations, such as parasitoidism, wasp-waist, sting, and secondary phytophagy. We also discovered the distinct genomic trajectories between the clade containing major parasitoid wasps (Parasitoida) and stinging species (Aculeata) since their divergence, which are involved in many aspects of genomic change, such as rapidly evolving gene families, gene gain and loss, and metabolic pathway evolution. In addition, we explored the genomic features accompanying the three independent evolution of secondary phytophagy. Our work provides insights for understanding genome evolution and the genomic basis of diversification in Hymenoptera.

genomics↗

bioRxiv2024

Enhanced purinergic signaling in the paraventricular hypothalamus induces hyperphagic obesity and insulin resistance

Body energy homeostasis is tightly regulated by hypothalamic neural circuits. However, their remodeling upon metabolic challenges remains incompletely characterized, thus complicating the development of safe medications against the surge of metabolic diseases. Oxytocin (OXT) neurons in the paraventricular nucleus of the hypothalamus (PVH) are one of the key effectors regulating energy balance. In this work, we report that high-fat diet (HFD) feeding in mice evokes spatiotemporally selective ATP release from astrocytes (Inflares) in the PVH, accompanied by the expression of hematopoietic lineage-specific ADP/ATP receptor P2Y12 on local OXT (PVHOXT) neurons. Strikingly, increased purinergic signaling leads to impaired responsiveness of PVHOXT neurons accompanied by hyperphagic obesity and insulin resistance in mice. Conversely, loss of P2Y12 in PVHOXT neurons attenuates metabolic phenotypes, illustrating that such remodeling is both necessary and sufficient to induce metabolic phenotypes. Inflares were also induced by hyperglycemia, while emergence of P2Y12 on OXT neurons of patients with diabetes mellitus suggests an evolutionary conserved purinergic response to various metabolic challenges and its potential as a drug target. Accordingly, nasal administration of clinically approved doses of P2Y12 inhibitors counteracts obesity in mice and non-human primates, paving the way for application of these compounds in patients with metabolic disorders.

neuroscience↗

bioRxiv2024

Bird brains fit the bill: morphological diversification and the evolution of avian brain size

Brain size varies greatly across and even within lineages. Attempts to explain this variation have mostly focused on the role of specific cognitive demands in the social or ecological domain. However, their predictive power is modest, whereas the effects of additional functions, especially sensory information processing and motor control, on brain size remain underexplored. Here, using phylogenetic comparative models, we show that the socio-cognitive and eco-cognitive demands do not have direct links to relative brain size (that is the residual from a regression against body mass) once morphological features are taken into account. Thus, specific cognitive abilities linked to social life or ecology play a much smaller role in brain size evolution than generally assumed. Instead, parental provisioning, generation length, and especially eye size and beak and leg morphology have a strong direct link to relative brain size. Phylogenetic lability analyses suggest that morphological diversification preceded changes in the rate of brain size evolution and greater visual input, and thus that morphological diversification opened up specialized niches where efficient foraging could produce energy surpluses. Increases in brain size provided general behavioural flexibility, which improved survival by reducing interspecific competition and predation, and was made possible by intense parental provisioning. Indeed, comparative analyses in a subset of species show that thicker beaks are associated with larger size of brain regions involved in behavioural flexibility (telencephalon, pallium). Thus, morphological evolution had a key role in niche diversification, which subsequently may have facilitated the evolution of general cognitive flexibility.

evolutionary biology↗