Biology subjects

Yang, Q.

Publications and source records attributed to Yang, Q..

At least 163 records · Page 9Linked to original sources

bioRxiv2024

Approximate Bayesian computation supports a high incidence of chromosomal mosaicism in blastocyst-stage human embryos

Chromosome mis-segregation is common in human meiosis and mitosis, and the resulting aneuploidies are the leading cause of pregnancy loss. Preimplantation genetic testing for aneuploidy (PGT-A) prioritizes chromosomally normal embryos for transfer based on analysis of a biopsy of approximately five trophectoderm cells from blastocyst-stage in vitro fertilized (IVF) embryos. While modern PGT-A platforms classify these biopsies as aneuploid, euploid, or mosaic (a mixture of normal and aneuploid cells), the underlying incidences of aneuploid, euploid, and mosaic embryos and the rates of meiotic and mitotic error that produced them remain largely unknown. To address this knowledge gap, we paired a method for embryo simulation with approximate Bayesian computation (ABC) to infer rates of meiotic and mitotic error that explain published PGT-A data. Using simulation, we also evaluated the chromosomal status of entire embryos. For a published clinical sample, we estimated a 40-58% probability of meiotic error per meiosis and a 1.5-6.3% probability of mitotic error per mitosis, depending on assumptions about spatial organization. In addition, our analyses suggest that less than 1% of blastocysts are fully euploid and that many embryos possess low-level mosaic clones that are not captured during biopsy. These conclusions were relatively insensitive to misclassification of mosaic biopsies. Together, our findings imply that low-level mosaicism is a normal feature of embryogenesis and are consistent with clinical data demonstrating the developmental potential of mosaic-testing embryos. More broadly, our work helps overcome the limitations of embryo biopsies to estimate fundamental rates of chromosome mis-segregation in human development. SummaryChromosome errors are the main cause of human pregnancy loss. Researchers used computer simulations and statistics to estimate the rates of these errors based on published clinical data from in vitro fertilized embryos. To explain data, the researchers estimated that 40-58% of cell divisions that produced the egg or sperm were affected by an error, along with 1.5-6.3% of cell divisions after fertilization. Their results also showed that fewer than 1% of embryos are completely normal in all cells and that many embryos contain small groups of abnormal cells that testing often misses. These findings improve understanding of early development.

genetics↗

bioRxiv2024

An immunomechanical checkpoint PYK2 governs monocyte-to-macrophage differentiation in pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) is characterized by a fibrotic, stiff tumor microenvironment (TME), where tumor-associated macrophages (TAMs) drive ECM remodeling, progression, and immune evasion. The contribution of mechanical cues to monocyte differentiation into TAMs remains largely unexplored. Here we show that mechanical force is required for monocyte-to-macrophage differentiation. PYK2, as an innovative immunomechanical checkpoint, de facto governs this differentiation process. We demonstrated that PYK2 senses mechanical signals via Piezo1 and integrins, triggering F-actin polymerization and translocating to the nucleus to regulate mechanotransduction and differentiation genes (e.g., ACTR3, RELA). Targeted deletion of PYK2 impairs the differentiation and polarization of monocyte-derived macrophages, reshapes the PDAC microenvironment, and enhances the efficacy of anti-PD-1 immunotherapy. These findings underscore the critical role of mechanical cues in monocyte differentiation and suggest that targeting PYK2 is a promising strategy to modulate TAM function and improve immunotherapy outcomes in patients with PDAC. Statement of significanceThis study identifies PYK2 as an immunomechanical checkpoint that drives monocyte-to-macrophage differentiation in PDAC via Piezo1/integrin-mediated mechanical cues. Targeted deletion of PYK2 reshapes the PDAC microenvironment, and enhances the efficacy of anti-PD-1 immunotherapy, suggesting PYK2 as a promising therapeutic target to overcome immunotherapy resistance.

immunology↗

bioRxiv2024

Characteristic of KPC-14, a KPC Variant Conferring Resistance to Ceftazidime-Avibactam in the Extensively Drug-resistant ST463 Pseudomonas aeruginosa Clinical Isolate

We studied two KPC-14 variants from clinical Pseudomonas aeruginosa isolates, C137 and C159, to better understand genomic diversity, mechanisms, and genes that confer antibiotic resistance and pathogenicity. C137 and C159, a sequence type 463 ExoU-positive multidrug-resistant strain, were concurrently resistant to carbapenems and ceftazidime-avibactam (CZA). Both strains possessed five intrinsic antimicrobial resistance genes (fosA, catB7, crpP, blaPAO, and a blaOXA-486 variant), as well as the blaKPC-14 gene in the chromosome. In strain C137, blaKPC-14 gene was situated on the plasmid pC137. KPC-14-harbouring transformants of pC137 exhibited resistance to CZA and restored sensitivity to carbapenems, signifying a "see-saw" effect. Both strains demonstrated the expression of the blaKPC-14 gene, concurrent inactivation of the outer membrane protein OprD, overexpression of the efflux pump MexX, and a pronounced capacity for biofilm formation. The genomic environment of KPC-14 consisted of IS26/IS26/TnpR_Tn3/ISKpn27/ISKpn6/IS26, which was classified as pseudo-compound transposons (PCTs). Plasmid pC137 closely resembled the previously described plasmid p94, which possesses the same genomic architecture, implying that IS26-mediated PCTs may store a variety of resistance genes, including blaKPC-2 and KPC variants, and were currently disseminating in the region. The KPC-14 variant presents significant challenges for clinical treatment. The blaKPC-14 gene, carried by the PCTs, was integrated into the chromosome, exhibiting stability throughout bacterial inheritance. Our research highlights the necessity for improved clinical surveillance of Klebsiella pneumoniae carbapenemase-producing P. aeruginosa.

molecular biology↗

bioRxiv2024

Mesenchymal Cell-Derived Extracellular Vesicles Ameliorate Age-Related Deficits in Working Memory as well as Brain MRI and CSF in vivo Biomarkers of Neurodegeneration in Rhesus Monkeys.

Normal aging in humans and non-human primates is associated with a decline in cognitive functions. Subject-wise differences in cognitive decline can be attributed to different degrees of damage to cortical white matter (WM) which is largely affected by neuroinflammation during aging. Mesenchymal stromal cell-derived extracellular vesicles (MSC-EVs) have recently been identified as a potential immunomodulatory therapeutic for brain damage and Alzheimers disease (AD) and related dementias by suppressing neuroinflammation. Here, we evaluated the efficacy of MSC-EVs for slowing or ameliorating cognitive decline during aging in rhesus monkeys, a well-studied model of normal aging that is free of extensive AD pathology. We report that late middle-aged monkeys treated with MSC-EVs every two weeks for 18 months showed improved performance on a task of spatial working memory relative to vehicle control monkeys. In addition, we used diffusion magnetic resonance imaging (MRI) and resting state functional MRI to evaluate structural white matter and functional network changes in vivo. Imaging data revealed that MSC-EV treatment preserved prefrontal and temporal WM structural integrity and large-scale functional network connectivity that are correlated with early, increased CSF levels of amyloid beta protein. Amyloid beta levels at 12 months are also correlated with improved cognitive performance at the end of the 18 months of treatment. These findings suggest that MSC-EVs can mitigate age-related cognitive decline by potentially enhancing the CSF clearance of neurodegenerative proteins, which correlates with greater WM integrity and functional brain connectivity.

neuroscience↗

bioRxiv2024

Unraveling Keystone Taxa: Interactions Within Microbial Networks and Environmental Dynamics in Lake Mendota

Microbial communities in freshwater ecosystems drive critical biogeochemical cycles, nutrient transformations, and energy flows essential for ecosystem stability. Yet, in the face of accelerating environmental changes, the responses of these microbial networks to spatial and temporal shifts remain underexplored, particularly with rising anoxia. We investigated the microbial ecosystems of Lake Mendota, Wisconsin, USA, through comprehensive metagenomic and metatranscriptomic analyses to elucidate their adaptations to environmental fluctuations across temporal and spatial dimensions. Employing tools like Sparse Inverse Covariance Estimation for Ecological Association Inference (SPIEC-EASI) and Conditional Auto-Regressive Least Absolute Shrinkage and Selection Operator (CARlasso), we identified key microbial taxa and their interactions with environmental parameters such as depth, temperature, pH, and dissolved oxygen. Our findings reveal that biological interactions more than environmental variables shape microbial community assembly and function. Specifically, keystone taxa from the phylum Bacteroidota emerged as pivotal in nutrient cycling and organic matter decomposition, processes crucial for sustaining water quality. Notably, these keystone taxa demonstrate dynamic adaptability, suggesting that microbial networks can rapidly adjust to changes in composition, a trait essential for resilience in the face of warming temperatures and altered precipitation patterns. This study provides critical insights into the resilience and adaptability of freshwater microbiomes, highlighting the role of microbial interactions in maintaining ecosystem health. By understanding how these microbial networks respond to environmental pressures, we can better predict shifts in microbial dynamics and anticipate the broader ecological impacts of climate change on freshwater systems. ImportanceThis research underscores the critical role of keystone taxa in freshwater ecosystems, highlighting how these organisms maintain water quality and contribute to the stability of aquatic environments. Understanding the ecological roles of these taxa is essential for developing strategies to manage ecosystems and conserve freshwater resources, particularly in the face of ongoing environmental challenges like climate change. The insights provided by this study not only enhance our comprehension of microbial interactions but also support effective ecosystem management and conservation efforts.

microbiology↗

bioRxiv2024

Mutations of schizophrenia risk gene SETD1A dysregulate synaptic function in human neurons

Schizophrenia (SCZ) is a complex neuropsychiatric disorder associated with both common risk variants of small effect sizes and rare risk variants of high penetrance. Rare protein truncating variants (PTVs) in SETD1A (SET Domain Containing 1A) show a strong association with SCZ; however, it remains largely unclear how rare PTVs in SETD1A contribute to the pathophysiology of SCZ. To understand the impact of SETD1A rare PTVs in human neurons, we CRISPR/Cas9-engineered five isogenic pairs of human induced pluripotent stem cells (iPSCs), with a recurrent heterozygous patient-specific PTV mutation c.4582-2delAG in two donor lines and a heterozygous frameshift mutation c.4596_4597insG (p. Leu1533fs) in three donor lines. These two mutations are predicted to cause a premature stop codon in exon 16 of SETD1A, leading to the loss of the conserved SET domain that is critical for its histone methyltransferase activity. We found that these presumably loss-of-function (LoF) mutations caused the SETD1A mRNAs to be degraded by nonsense-mediated decay (NMD), accompanied by a reduction of full-length SETD1A protein level in iPSCs. We then characterized the morphological, electrophysiological, and transcriptomic impacts of the SETD1A+/- LoF mutations in iPSC-derived human excitatory neurons induced by NGN2. We found that the SETD1A+/- exon-16 LoF mutations altered dendrite complexity, dysregulated synaptic transmission, and synaptic plasticity, likely by dysregulating genes involved in synaptic function. These results provide mechanistic insights into how SETD1A+/-exon-16 patient-specific LoF mutations affect neuron phenotypes that may be relevant to the pathophysiology of SCZ.

neuroscience↗

bioRxiv2024

OfWRKY33 binds to the key linalool synthase gene OfTPS7 to promote linalool synthesis in Osmanthus fragrans flowers

Volatile aroma compounds make significant contributions to human perception of flowers. Osmanthus fragrans is a famous aroma plant and linalool along with its oxides are proved to be the dominant aroma active compounds. Although some terpene synthases (TPSs) have been characterized, a comprehensive study of the hub metabolic gene and its transcriptional regulation remain to be revealed. Here, we selected a specific cultivar Boyeyingui (BBYG) with the highest content of linalool among 20 wide-cultivated cultivars for genome and transcriptome sequencings. Among the 25 new putative OfTPSs, only OfTPS6, OfTPS7 could exclusively produce linalool in planta. Biochemical analysis demonstrated that OfTPS6, OfTPS7 were able to catalyze geranyl diphosphate (GPP) into linalool and a small proportion of other monoterpenes in vitro. Spatial and temporal correlation analysis further confirmed the transcript level of OfTPS7 was closely associated with linalool content in diverse cultivars and different tissues, suggesting OfTPS7 was the essential linalool synthase gene. Combined with yeast one-hybrid screen and weighted correlation network analysis (WGCNA), a nucleus-localized transcriptional factor OfWRKY33 was considered as a potential modulator. Y1H, dual-luciferase assay and electrophoretic mobility shift assay (EMSA) demonstrated that OfWRKY33 directly bound to the W-box of OfTPS7 promoter to stimulate its transcription. OfWRKY33 could coordinately induce the expressions of OfTPS7, 1-deoxy-d-xylulose 1 (OfDXS1), thereby promoting the linalool formation. The results first revealed the hub linalool synthase gene OfTPS7 and a novel TF participating in the complex transcriptional regulation of linalool biosynthesis in O. fragrans flowers.

biochemistry↗

bioRxiv2024

DEMINERS enables clinical metagenomics and comparative transcriptomic analysis by increasing throughput and accuracy of nanopore direct RNA sequencing

Nanopore direct RNA sequencing (DRS) advances RNA biology but is limited by relatively low basecalling accuracy, low throughput, yet high RNA input and costs. Here we introduce a novel DRS toolkit, DEMINERS, which integrates an RNA multiplexing experimental workflow, a machine-learning barcode classifier based on Random Forest and a novel basecaller built on an optimized convolutional neural network providing an additional species-specific training module. With the increased accuracy in barcode classification and basecalling, DEMINERS can demultiplex up to 24 samples and the required RNA input and running time are both substantially reduced. We demonstrated the applications of DEMINERS in clinical metagenomics, cancer transcriptomics and parallel comparison of transcriptomic features in different biological conditions, revealing altered airway microbial diversity in COVID-19 and a potential role of m6A in increasing transcriptomic diversity in glioma and the mature blood-stage of malaria parasites. Overall, DEMINERS is a simple, robust, high-throughput DRS method for accurately estimating transcript levels, poly(A) lengths, and mutation and RNA modification heterogeneity at single-read level, with minimal sequencing biases.

bioinformatics↗

bioRxiv2024

Global patterns, drivers and impacts of metabolic traits across amniotes

Metabolism and climate are thought to influence species richness and diversification, yet few studies have examined whether global patterns of metabolic traits are linked to climate and diversification rate. Here we investigate the drivers of global metabolic rates and their impacts on biodiversity across 2,633 amniote vertebrates. We found consistent distribution patterns of metabolic rates in terrestrial amniotes and marine birds, with metabolic rates increasing with distance from the equator across latitudes. Temperature is a primary climatic variable affecting metabolic rates in birds and mammals, whereas precipitation dominates in terrestrial reptiles. Furthermore, elevated metabolic rates promote diversification rates and reduce extinction risks in birds and terrestrial mammals. Conversely, high metabolic rates decrease diversification rates and increase extinction risks in reptiles. Our results show that global patterns of metabolic rates are driven by various climate variables and may shape diversification and extinction patterns among amniotes in the context of climate change.

ecology↗

bioRxiv2024

Identification and characterization of ugpE required for the full virulence of Streptococcus suis

Streptococcus suis (S. suis) is an emerging zoonotic pathogen that threatens both animal and human health worldwide. UgpE is a protein subunit of the Ugp (uptake of glycerol phosphate) transporter system that is involved in glycerophospholipid synthesis in bacterial membranes. In this study, an ugpE deletion mutant was constructed and the effects of ugpE deletion on cell morphology, biofilm formation, and virulence were investigated. Deletion of ugpE did not affect bacterial growth but impaired cell chain formation and capsular synthesis by downregulating the mRNA levels of the capsular regulon genes cps-2B, cps-2C, and cps-2S. Deletion of ugpE also led to decreased tolerance to heat, oxidative, and acid-base stress. Crystal violet staining and scanning electron microscopy demonstrated ugpE negatively regulated biofilm formation in liquid culture and the rdar biofilm morphotype on agar plates. Moreover, ugpE deletion not only reduced hemolysin activity, survival in whole human blood, and anti-phagocytosis ability against porcine alveolar macrophages (PAM) but also enhanced bacterial adhesion and invasion of human cerebral microvascular endothelial cells (hCMEC/D3) by upregulating the expression of multiple genes associated with cell adhesion. In a mouse infection model, ugpE deletion significantly attenuated virulence and lowered the number of viable bacteria in the blood and major organs, as well as distribution of macrophages. In conclusion, this study identified UgpE as a novel virulence factor that plays a pivotal role in the regulation of virulence and biofilm formation of S. suis.

microbiology↗

bioRxiv2024

A persistent bacterial Regiella transinfection in the bird cherry-oat aphid Rhopalosiphum padi increasing host fitness and decreasing plant virus transmission

The bird cherry-oat aphid, Rhopalosiphum padi, is a major pest of agriculture due to its ability to directly damage crops and transmit plant viruses. As industries move away from chemical pest control, there is interest in exploring new options to suppress the impact of this pest. Here we describe the production of a transinfected line of R. padi carrying the bacterial endosymbiont, Regiella insecticola, originating from the green peach aphid, Myzus persicae. We show that Regiella increases the fitness of its novel host despite decreasing fitness in its native host. Regiella also shows a low level of horizontal transmission. Importantly the infection suppresses the ability of R. padi to transmit the barley yellow dwarf virus which damages wheat plants. This transinfection could be released to suppress virus transmission by aphids with its ability to persist and spread, making it potentially suitable for wide area release.

microbiology↗

bioRxiv2024

Endosymbionts impact ladybird predation rates of aphids in a temperature-dependent manner

Aphids are worldwide pests causing major economic losses to growers. Current management strategies rely heavily on pesticides, but some effective pesticides are being withdrawn and the efficiency of remaining pesticides is also decreasing as aphids build up resistance. Biological control using predators can provide a sustainable alternative to pesticides under some circumstances, while the deliberate introduction of facultative bacterial endosymbionts that induce host fitness costs and reduce plant virus transmission provides another potential future strategy to combat aphid pests. However, new control options should not be antagonistic, with the concern that the effectiveness of biocontrol might be altered by endosymbiont presence in hosts. We, therefore, tested if predation by two aphidophagous ladybirds, Adalia bipunctata and Harmonia conformis, on the green peach aphid, Myzus persicae, and the oat aphid, Rhopalosiphum padi, was affected by transinfected Rickettsiella viridis and both native and transinfected Regiella insecticola endosymbionts at different temperatures. The predation rate of aphids infected by either endosymbiont was higher at 14 {degrees} C than the rate for uninfected aphids of both species, but the opposite pattern was apparent at 20 {degrees}C and for one host-endosymbiont combination at 26 {degrees}C. Overall, the results showed that higher temperatures increased predation, while differences between intermediate and low temperatures were species-dependent. No transmission of endosymbionts from aphid to ladybird through predation was detected. These findings point to a lack of consistent effects of the investigated endosymbionts on predation rates in these major aphid pests. The temperature dependence of endosymbiont-predation interactions suggests that the impact of seasonal climate should be considered when assessing the potential of endosymbionts in a biological control setting. HIGHLIGHTS- Aphid endosymbiont effects on ladybird predation rates are temperature-dependent - Ladybird predation rate of aphids increases as temperature rises - Prey (aphid) endosymbionts are not transferred to predators (ladybirds)

ecology↗

bioRxiv2024

The endosymbiont Rickettsiella viridis increases the virulence of Diuraphis noxia but reduces alate frequency

Aphids are among the worlds most economically damaging pests and carry a diverse range of bacterial endosymbionts. There is increasing interest in exploring potential applications of natural and novel strains of endosymbionts in aphid control. One endosymbiont, Rickettsiella viridis, has a large fitness cost following transfer from its natural aphid host Acyrthosiphon pisum into a novel host aphid Myzus persicae. Here, we investigated host impacts after transferring the same Rickettsiella strain to an important cereal aphid, the Russian wheat aphid Diuraphis noxia. Rickettsiella in this host resulted in modest fitness effects, with a minor increase in heat tolerance and a decrease in development time at 25{degrees} C. The infection persisted in mixed caged populations under different temperatures. Surprisingly, Rickettsiella increased aphid virulence to wheat plants and to two non-crop hosts of D. noxia, barley grass and brome grass. This was evident from sharper decreases in leaf number and leaf area, as well as an increase in chlorotic streaking when plants were exposed to Rickettsiella-infected D. noxia. Rickettsiella also reduced the proportion of alates in aphids held in small cages and in larger mesocosms containing multiple wheat plants where short-distance dispersal of aphids was impacted. These results provide compelling evidence that Rickettsiella can affect virulence - the first case of an endosymbiont transfer directly influencing aphid virulence to host plants - and highlight the species-specific impacts of endosymbiont transfers on aphids which can involve multiple traits.

microbiology↗

bioRxiv2024

Toxoplasma gondii transcription factor AP2XII-8: a key regulator of G1 phase progression and parasite division

The apicomplexan parasite Toxoplasma gondii can infect humans and virtually all warm-blooded animals worldwide, posing a significant threat to public health and being of veterinary importance. Acute infections are characterized by the fast replication of tachyzoites inside host cells. During this fast amplification process, gene expression is highly regulated by a series of regulatory networks. The G1 phase, which is usually conserved across species, is responsible for preparing the materials necessary for the next replicating cell cycle; however, few regulators have been identified at this stage. Here, we functionally characterized the C/G1 phase-expressed ApiAP2 transcription factor, TgAP2XII-8, in T. gondii tachyzoites. Conditional knockdown of TgAP2XII-8 leads to significant growth defects and asexual division disorders. Additionally, parasite cell cycle progression was disrupted following TgAP2XII-8 depletion, characterized by G1 phase arrest. RNA-seq and CUT&Tag experiments revealed that TgAP2XII-8 acts as an activator of ribosomal proteins expressed in the G1 phase. Moreover, TgAP2XII-8 binds to a specific DNA motif ([T/C]GCATGCA), which is abundant and conserved in the intergenic region of several other apicomplexans, possibly suggesting a broad and conserved role for this ApiAP2 in the Phylum of Apicomplexa. Our study reveals that TgAP2XII-8 acts as a critical C/G1 phase regulator, orchestrating the cell cycle in T. gondii tachyzoites. This study contributes to a broader understanding of the complexity of the parasites cell cycle and its key regulators.

microbiology↗

bioRxiv2024

Rapamycin alters the feeding preference for amino acids and sugar in female Drosophila

Pharmacological interventions targeting the aging process hold significant promise for improving the quality of life in the elderly and reducing healthcare costs. Rapamycin, in particular, has exhibited significant anti-aging and lifespan-extending effects across multiple model organisms. However, chronic rapamycin administration may also lead to various adverse reactions since it reshapes energy metabolism. Here, using Drosophila melanogaster as a model, we show that life-prolonging doses of rapamycin significantly modify animal feeding behavior. Long-term administration of rapamycin decreased protein preference in females while enhancing their sugar intake. Utilizing a chemically defined diet, we identified that changes in amino acid and sugar feeding preferences emerged as early as the second day of rapamycin treatment, preceding any detectable decline in fecundity. However, rapamycin-induced changes in macronutrient feeding preferences were not observed in males and sterile mutant females. Overall, our study suggests that the modification of feeding behavior could be a non-negligible side effect of rapamycin treatment, which is influenced by both sex and reproductive status.

animal behavior and cognition↗

bioRxiv2024

Neural Circuit Underlying Individual differences in Visual Escape Habituation

Emotions, like fear, are internal states enabling organisms to effectively confront environmental threats. When repeatedly exposed to predators, individuals show divergent adaptive responses. However, the neural circuit mechanisms underlying individual differences in to repeated threats remain largely unknown. Here, we identify two distinct types of visual escape--consistent escape (T1) and rapid habituation (T2) -- with unambiguous arousal states to repetitive threat stimuli. We systematically investigate distinct pathways originating from the superior colliculus (SC) and insula that project to the basolateral amygdala (BLA), with relay stations in the mediodorsal thalamus (MD) and ventral tegmental area (VTA), mediating T1 and T2 behavioral types. Additionally, we identify the MD as a critical hub integrating SC and insula inputs, projecting to the BLA and contributing to reduced arousal and attenuated defensive behaviors against looming stimuli. Our findings offer significant insights into the mechanisms of internal states, arousal modulation, and behavioral adaptability. O_FIG O_LINKSMALLFIG WIDTH=178 HEIGHT=200 SRC="FIGDIR/small/611366v1_ufig1.gif" ALT="Figure 1"> View larger version (77K): org.highwire.dtl.DTLVardef@164df34org.highwire.dtl.DTLVardef@17a01e6org.highwire.dtl.DTLVardef@112de44org.highwire.dtl.DTLVardef@1be6aea_HPS_FORMAT_FIGEXP M_FIG Graph Abstract C_FIG In briefWe identify two distinct visual escape behaviors--consistent escape (T1) and rapid habituation (T2)--linked to unique SC and insula pathways projecting to the BLA via MD and VTA. The MD acts as a hub integrating sensory inputs to modulate arousal and defensive responses. These findings advance our understanding of the neural mechanisms driving internal states, arousal modulation, and behavioral adaptability. Highlights[bullet] We identify two distinct visual escape behaviors with unambiguous arousal states--consistent escape (T1) and rapid habituation (T2) --to repeated looming stimuli. [bullet]The SC-VTA-BLA pathway mediated T1 behavioral type, while the SC-MD-BLA pathway mediated T2 type. [bullet]MD as a central hub integrating SC and insula inputs to modulate arousal and defensive behavioral adaptation.

neuroscience↗

bioRxiv2024

Discovery of novel quinoline papain-like protease inhibitors for COVID-19 through topology constrained molecular generative model

The rapid emergence of drug-resistant SARS-CoV-2 variants poses a persistent challenge to current antiviral strategies. Mutations in key viral targets, including RNA-dependent RNA polymerase (RdRp), main protease (3CLpro), and papain-like protease (PLpro), have been shown to markedly reduce the efficacy of approved therapeutics, highlighting the urgent need for next-generation antivirals capable of overcoming resistance. Here, we report the discovery of a novel class of PLpro inhibitors through an AIDD strategy based on a topology-constrained molecular generative model (Tree-Invent) integrated with structure-guided optimization. Scaffold hopping from a previously reported lead enabled the identification of a quinoline-based chemical series with substantially improved metabolic stability and antiviral potency. Structure-guided optimization yielded compound GZNL-2016, which exhibited potent enzymatic inhibition of PLpro (IC50 = 10.5 nM), robust antiviral activity against multiple SARS-CoV-2 variants, including Omicron BA.5 and XBB.1, and favorable pharmacokinetic properties following oral administration. Notably, GZNL-2016 retained substantial inhibitory activity against the clinically relevant drug-resistant mutant PLpro E167K (IC50 = 480.2 nM; Ki = 439.3 nM), in contrast to previously reported inhibitors that exhibit markedly reduced potency. In a SARS-CoV-2 infection mouse model, oral administration of GZNL-2016 significantly reduced pulmonary viral titers, demonstrating in vivo antiviral efficacy. Collectively, this study establishes an AI-enabled strategy for rapid antiviral discovery and identifies GZNL-2016 as a promising lead compound to address the threat of coronavirus infections caused by drug-resistant mutant SARS-CoV-2 variants. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/611841v3_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@ecbd3eorg.highwire.dtl.DTLVardef@7c663corg.highwire.dtl.DTLVardef@11c0e37org.highwire.dtl.DTLVardef@e950f0_HPS_FORMAT_FIGEXP M_FIG C_FIG We leveraged an AI generative model to discover a novel PLpro inhibitor with excellent liver stability, low CYP, hERG inhibition and reasonable oral PK properties. At the same time, the compound 16 exhibits high efficacy for the resistance mutation E167K, which resulted in severe resistance to the previously reported inhibitor Jun12682 and PF-07957472.

microbiology↗

bioRxiv2024

Conserved role of spike S2 domain N-glycosylation across beta-coronavirus family

Besides acting as an immunological shield, the N-glycans of SARS-CoV-2 are also critical for viral life cycle. As the S2 subunit of spike is highly conserved across beta-coronaviruses, we determined the functional significance of the five stem N-glycans located in S2 between N1098-N1194. Studies were performed with 31 Asn-to-Gln mutants, beta-coronavirus virus-like particles and single-cycle viral replicons. Deletions of stem N-glycans enhanced S1 shedding from trimeric spike, reduced ACE2 binding and abolished syncytia formation. When three or more N-glycans were deleted, spike expression on cell surface and incorporation into virions was both reduced. Viral entry function was progressively lost upon deleting the N1098 glycan in combination with additional glycosite modifications. In addition to SARS-CoV-2, deleting stem N-glycans in SARS-CoV and MERS-CoV spike also prevented viral entry into target cells. These data suggest multiple functional roles for the stem N-glycans, and evolutionarily conserved properties for these complex carbohydrates across human beta-coronaviruses. Author SummaryPrevious work shows that the N-linked glycans of SARS-CoV-2 are essential for viral life cycle. Few natural mutations have been observed in the S2-subunit of the viral spike glycoprotein in GISAID data, and mutations are absent in the five stem N-glycans located between N1098-N1194. In the post-fusion spike structure these glycans lie equidistant, ~4 nm apart, suggesting functional significance. Upon testing the hypothesis that these glycans are critical for SARS-CoV-2 function, we noted multiple roles for the complex carbohydrates including regulation of S1-subunit shedding, spike expression on cells and virions, syncytial formation/cell-cell fusion and viral entry. Besides SARS-CoV-2, these glycans were also critical for other human beta-coronaviruses. Thus, these carbohydrates represent targets for the development of countermeasures against future outbreaks.

microbiology↗