Biology subjects

Sun, H.

Publications and source records attributed to Sun, H..

At least 217 records · Page 12Linked to original sources

bioRxiv2023

Long-Term In Vivo Molecular Monitoring Using Aptamer-Graphene Microtransistors

Long-term, real-time molecular monitoring in complex biological environments is critical for our ability to understand, prevent, diagnose, and manage human diseases. Aptamer-based electrochemical biosensors possess the promise due to their generalizability and a high degree of selectivity. Nevertheless, the operation of existing aptamer-based biosensors in vivo is limited to a few hours. Here, we report a first-generation long-term in vivo molecular monitoring platform, named aptamer-graphene microtransistors (AGMs). The AGM incorporates a layer of pyrene- (polyethylene glycol)5-alcohol and DNase inhibitor-doped polyacrylamide hydrogel coating to reduce biofouling and aptamer degradation. As a demonstration of function and generalizability, the AGM achieves the detection of biomolecules such as dopamine and serotonin in undiluted whole blood at 37 {degrees}C for 11 days. Furthermore, the AGM successfully captures optically evoked dopamine release in vivo in mice for over one week and demonstrates the capability to monitor behaviorally-induced endogenous dopamine release even after eight days of implantation in freely moving mice. The results reported in this work establish the potential for chronic aptamer-based molecular monitoring platforms, and thus serve as a new benchmark for molecular monitoring using aptamer-based technology.

bioengineering↗

bioRxiv2023

Engineered dsRNA-protein nanoparticles for effective long-distance transport, delivery and gene silencing in plants

Long-distance transport of exogenous biologically active RNA molecules in higher plants has not been reported. Here, we report that cationized bovine serum albumin (cBSA) avidly binds double-stranded beta-glucuronidase RNA (dsGUS RNA) to form nucleic acid-protein nanocomplexes. Using tobacco and poplar plants, we have shown effective uptake and long-distance transport of cBSA/dsGUS RNA nanocomplexes from basal ends of leaf petioles to leaf blades as well as from basal ends of shoots to their apexes and apical leaves. We have further demonstrated that the cBSA/dsGUS RNA nanocomplexes are highly effective in silencing both conditionally inducible DR5-GUS gene and constitutively active 35S-GUS gene in leaf, shoot and shoot meristem tissues. This cBSA/dsRNA delivery technology may provide a convenient, fast, and inexpensive tool for characterizing gene functions in plants, and potentially for in planta gene-editing.

molecular biology↗

bioRxiv2023

Aminoglycoside heteroresistance in Enterobacter cloacae is driven by the cell envelope stress response.

Enterobacter cloacae is a Gram-negative nosocomial pathogen of the ESKAPE priority group with increasing multi-drug resistance via the acquisition of resistance plasmids. However, E. cloacae can also display phenotypic antimicrobial resistance, such as heteroresistance or persistence. Here we report that E. cloacae ATCC 13047 and six strains isolated from patients with blood infections display heteroresistance or persistence to aminoglycosides. E. cloacae heteroresistance is transient, accompanied with formation of petite colonies and increased MIC against gentamicin and other aminoglycosides used in the clinic, but not other antibiotic classes. To explore the underlying mechanisms, we performed RNA sequencing of heteroresistant bacteria, which revealed global gene-expression changes and a signature of the CpxRA cell envelope stress response. Deletion of the cpxRA two-component system abrogated aminoglycoside heteroresistance and petite colony formation, pointing to its indispensable role in phenotypic resistance. The introduction of a constitutively active allele of cpxA led to high aminoglycoside MICs, consistent with cell envelope stress driving these behaviours in E. cloacae. Cell envelope stress can be caused by environmental cues, including heavy metals. Indeed, bacterial exposure to copper increased gentamicin MIC in the wild type, but not the {Delta}cpxRA mutant. Moreover, copper exposure also elevated the gentamicin MICs of bloodstream isolates, suggesting that CpxRA- and copper-dependent aminoglycoside resistance is broadly conserved in E. cloacae strains. Altogether, we establish that E. cloacae relies on transcriptional reprogramming via the envelope stress response pathway for transient resistance to a major class of frontline antibiotic. ImportanceEnterobacter cloacae is a bacterium that belongs to the ESKAPE priority group and an increasing threat worldwide due its multidrug resistance. E. cloacae can also display phenotypic resistance to antibiotics, leading to treatment failure. We report that sensitive strains of E. cloacae, including six strains isolated from patients with bloodstream infections, show heteroresistance or persistence to aminoglycoside antibiotics. These are important frontline microbicidal drugs used against Gram-negative bacterial infections, therefore understanding how resistance develops in sensitive strains is important. We show that aminoglycoside resistance is driven by the activation of the cell envelope stress response and transcriptional reprogramming via the CpxRA two-component system. Further, heterologous activation of envelope stress via copper, typically a heavy metal with antimicrobial actions, also increased aminoglycoside MICs in all tested strains of E. cloacae. Our study suggests phenotypic aminoglycoside resistance in E. cloacae could be broadly conserved and cautions against the undesirable effects of copper.

microbiology↗

bioRxiv2023

Multi-omics analysis reveals novel interplays between intratumoral bacteria and glioma

Emerging evidence highlights the potential impact of intratumoral microbiota on cancer. However, the microbial composition and function in glioma remains elusive. Consequently, our study aimed to investigate the microbial community composition in glioma tissues and elucidate its role in glioma development. We parallelly performed microbial profiling, transcriptome sequencing and metabolomics detection on tumor and adjacent normal brain tissues obtained from 50 glioma patients. We employed immunohistochemistry, multicolor immunofluorescence and FISH staining to observe the presence and location of bacteria. Furthermore, an animal model was employed to validate the impact of key bacteria on glioma development. Six genera were found to be significantly enriched in glioma tissues compared to its adjacent normal brain tissues, including Fusobacterium, Longibaculum, Intestinimonas, Pasteurella, Limosilactobacillus and Arthrobacter. Both bacterial RNA and LPS were observed in glioma tissues. Multicolor immunofluorescence analysis showed higher bacterial LPS levels in tumor cells than in macrophages and in glioma tissue than in adjacent normal brain tissue. Integrated microbiomics, transcriptomics, and metabolomics revealed that genes associated with intratumoral microbes were enriched in multiple synapse-associated pathways and that metabolites associated with intratumoral microbes were (R)-N-methylsalsolinol, N-acetylaspartylglutamic acid, and N-acetyl-L-aspartic acid. Further mediation analysis suggested that intratumoral microbiome may affect the expression of neuron-related genes through bacteria-associated metabolites. In addition, a glioma mouse model suggested that Fusobacterium nucleatum promoted glioma growth by increasing the levels of N-acetylneuraminic acid and the expression levels of CCL2, CXCL1, and CXCL2. In conclusion, our findings shed light on the intricate interplays between intratumoral bacteria and glioma.

neuroscience↗

bioRxiv2023

An interface-based molecular generative framework for protein-protein interaction inhibitors

Protein-protein interactions (PPIs) play a crucial role in numerous biochemical and biological processes. Although several structure-based molecular generative models have been developed, PPI interfaces and compounds targeting PPIs exhibit distinct physicochemical properties compared to traditional binding pockets and small-molecule drugs. As a result, generating compounds that effectively target PPIs, particularly by considering PPI complexes or interface hotspot residues, remains a significant challenge. In this work, we constructed a comprehensive dataset of PPI interfaces with active and inactive compound pairs. Based on this, we propose a novel molecular generative framework tailored to PPI interfaces, named GENiPPI. Our evaluation demonstrates that GENiPPI captures the implicit relationships between the PPI interfaces and the active molecules, and can generate novel compounds that target these interfaces. Moreover, GENiPPI can generate structurally diverse novel compounds with limited PPI interface modulators. To the best of our knowledge, this is the first exploration of a structure-based molecular generative model focused on PPI interfaces, which could facilitate the design of PPI modulators. The PPI interface-based molecular generative model enriches the existing landscape of structure-based (pocket/interface) molecular generative model.

bioinformatics↗

bioRxiv2023

From head to tail - Atomistic mechanism of long-range coupling from the cytosolic sensor domain to the selectivity filter in TREK K2P channels

The two-pore domain potassium (K2P) channels TREK-1 and TREK-2 link neuronal excitability to a variety of stimuli including mechanical force, lipids, temperature and phosphorylation. This regulation involves the C-terminus as a polymodal stimulus sensor and the selectivity filter (SF) as channel gate. Using crystallographic up- and down-state structures of TREK-2 as a template for full atomistic molecular dynamics simulations, we reveal that the SF in down-state undergoes inactivation via conformational changes at the S1 ion coordination site, while the up-state structure maintains a stable and conductive SF. This provides an atomistic understanding of the low channel activity previously assigned to the down state, but not evident from the crystal structure. Furthermore, by using (de-)phosphorylation mimics and chemically attaching lipid tethers to the proximal C-terminus (pCt), we confirm the hypothesis that moving the pCt towards the membrane induces the up-state. We also uncover two gating pathways by which movement of the pCt controls the stability (i.e. conductivity) of the filter gate. Together, these findings provide atomistic insights into the SF gating mechanism and the physiological regulation of TREK channels by phosphorylation.

biophysics↗

bioRxiv2023

CaCO3 Nanoparticles Delivering MicroRNA-200c Suppress Oral Squamous Cell Carcinoma

MicroRNA (miR)-200c suppresses the initiation and progression of oral squamous cell carcinoma (OSCC), the most prevalent head and neck cancer with high recurrence, metastasis, and mortality rates. However, miR-200c-based gene therapy to inhibit OSCC growth and metastasis has yet to be reported. To develop an miR-based gene therapy to improve the outcomes of OSCC treatment, this study investigates the feasibility of plasmid DNA encoding miR-200c delivered via non-viral CaCO3-based nanoparticles to inhibit OSCC tumor growth. CaCO3-based nanoparticles with various ratios of CaCO3 and protamine sulfate (PS) were utilized to transfect pDNA encoding miR-200c into OSCC cells and the efficiency of these nanoparticles was evaluated. The proliferation, migration, and associated oncogene production, as well as in vivo tumor growth for OSCC cells overexpressing miR-200c were also quantified. It was observed that, while CaCO3-based nanoparticles improve transfection efficiencies of pDNA miR-200c, the ratio of CaCO3 to PS significantly influences the transfection efficiency. Overexpression of miR-200c significantly reduced proliferation, migration, and oncogene expression of OSCC cells, as well as the tumor size of cell line-derived xenografts (CDX) in mice. In addition, a local administration of pDNA miR-200c using CaCO3 delivery significantly enhanced miR-200c transfection and suppressed tumor growth of CDX in mice. These results strongly indicate that the nanocomplexes of CaCO3/pDNA miR-200c may potentially be used to reduce oral cancer recurrence and metastasis and improve clinical outcomes in OSCC treatment. (227 words)

bioengineering↗

bioRxiv2023

Host glutathione is required for Rickettsia parkeri to properly septate, avoid ubiquitylation, and survive in macrophages.

Spotted fever group Rickettsia obligately reside in the cytosol where they parasitize over fifty metabolites from their hosts. However, the role for metabolite acquisition in pathogenesis remains unclear. Here, we find that depletion of the abundant low molecular weight thiol glutathione led to an impaired ability of Rickettsia parkeri to form plaques. Super-resolution microscopy revealed that glutathione depletion with buthionine sulfoximine (BSO) in endothelial or epithelial cells led to the formation of bacterial chains that increased in length over time. Chained bacteria had fewer actin-tails and were impeded for their ability to spread from cell to cell. Glutathione depletion also caused an increased frequency of colocalization between the bacterial surface and polyubiquitin. R. parkeri was significantly more restricted upon glutathione depletion in primary macrophages than in epithelial cells in a mechanism that avoided activating the inflammasome and the production of type I interferon. Together, these data suggest that host glutathione is critical for rickettsial septation, actin-based motility, avoiding ubiquitylation, and survival in immune cells.

microbiology↗

bioRxiv2023

mTORC1/S6K1 signaling promotes sustained oncogenic translation through modulating CRL3IBTK-mediated non-degradative ubiquitination of eIF4A1

Enhanced protein synthesis is a crucial molecular mechanism that allows cancer cells to survive, proliferate, metastasize, and develop resistance to anti-cancer treatments, and often arises as a consequence of increased signaling flux channeled to mRNA-bearing eukaryotic initiation factor 4F (eIF4F). However, the post-translational regulation of eIF4A1, an ATP-dependent RNA helicase and subunit of the eIF4F complex, is still poorly understood. Here, we demonstrate that IBTK, a substrate-binding adaptor of Cullin 3-RING ubiquitin ligase (CRL3) complex, interacts with eIF4A1. The non-degradative ubiquitination of eIF4A1 catalyzed by CRL3IBTK complex promotes cap-dependent translational initiation, nascent protein synthesis, oncogene expression, and tumor cell growth both in vivo and in vitro. Moreover, we show that mTORC1 and S6K1, two key regulators of protein synthesis, directly phosphorylate IBTK to augment eIF4A1 ubiquitination and sustained oncogenic translation. This link between the CRL3IBTK complex and the mTORC1/S6K1 signaling pathway, which is frequently dysregulated in cancer, represents a promising target for anti-cancer therapies. Statement of Significance: Overexpression of IBTK contributes to the process of tumorigenesis by amplifying translation, and represents a promising target for anti-cancer therapies.

cancer biology↗

bioRxiv2023

Engineering the ADDobody protein scaffold for generation of high-avidity ADDomer super-binders

Adenovirus-derived dodecamer (ADDomer) nanoparticles comprise 60 copies of Adenovirus penton base protein (PBP). ADDomer is thermostable, rendering the storage, transport and deployment of ADDomer-based therapeutics independent of a cold-chain. To expand the scope of ADDomer nanoparticles for new applications, we engineered ADDobodies. ADDobodies represent the crown domain of the PBP, genetically separated from its multimerization domain. We inserted heterologous sequences into hyper-variable loops in the crown domain. The resulting ADDobodies were expressed at high yields in Escherichia coli, are monomeric and maintain thermostability. We solved the X-ray structure of an ADDobody prototype validating our design. We demonstrated that ADDobodies can be used to select a specific binder against a target in in vitro selection experiments using ribosome display, with an enrichment factor of [~]104-fold in one selection round. We show that ADDobodies can be converted back into ADDomers by genetically reconnecting the selected ADDobody with the PBP multimerization domain from a different species, giving rise to a multivalent nanoparticle, called Chimera, confirmed by a 2.2 [A] structure determined by cryogenic electron microscopy (cryo-EM). Chimera comprises 60 binding sites, resulting in ultra-high, picomolar avidity to the target.

synthetic biology↗

bioRxiv2023

Genome analyses reveal the secondary metabolites potentially influence the geographical distribution of Fusarium pseudograminearum populations

Fusarium crown rot (FCR), caused by Fusarium pseudograminearum, significantly impacts wheat yield and quality in Chinas Huanghuai region. The rapid F. pseudograminearum epidemic and FCR outbreak within a decade remain unexplained. In this study, two high-quality, chromosome-level genomes of F. pseudograminearum strains producing 3-acetyl-deoxynivalenol (3AcDON) and 15-acetyl-deoxynivalenol (15AcDON) toxins were assembled. Additionally, 38 related strains were resequenced. Genomic differences such as single nucleotide polymorphisms (SNPs), insertions/deletions (indels), and structural variations (SVs) among F. pseudograminearum strains were analyzed. The whole-genome SNP locus based population classification mirrored the toxin chenotype (3AcDON and 15AcDON)-based classification, indicating the presence of genes associated with the trichothecene toxin gene cluster. Further analysis of differential SNP, indel, and SV loci between the 3AcDON and 15AcDON populations revealed a predominant connection to secondary metabolite synthesis genes. Notably, the majority of the secondary metabolite biosynthesis gene cluster (SMGC) loci were located in SNP-dense genomic regions, suggesting high mutability and a possible contribution to F. pseudograminearum population structure and environmental adaptability. This study provides insightful perspectives on the distribution and evolution of F. pseudograminearum, and for forecasting the spread of wheat FCR, thereby aiding in the development of preventive measures and control strategies.

microbiology↗

bioRxiv2023

Pleistocene glaciation advances the younger temporal dimension of species diversification in a major biodiversity hotspot

O_LIThe expansive Himalayan-Hengduan Mountains (HM) and Qinghai-Tibet Plateau (QTP) form a biodiversity hotspot imperiled by global change. The species diversity, resulting from myriad factors led to plant diversification from 10 million years ago till now. However, despite understanding speciation timing better, a lack of in-depth population-level studies and a dearth of organismal sampling among closely related species and populations leaves an incomplete view of diversification trends and biotic influences. C_LIO_LIWe delve into the complex factors influencing diversification through genomic and eco-morphological analysis within the Stellera chamaejasme L. complex, known for its significant floral diversity. C_LIO_LIOur results uncover four cryptic species, indicating a more recent and younger diversification period ([~]2.67-0.9 Mya), driven by Pleistocene glaciation and a complex set of interacting biotic factors. These factors prompted allopatric speciation and advocated cyclical warming-cooling episodes along latitudinal and altitudinal gradients throughout the Pleistocene. C_LIO_LIThe study emphasizes the existence of cryptic species within these mountains, broadening our understanding of species diversification to more recent than previously recognized. This novel perspective may reshape evolutionary paradigms in plant science. Additionally, it also brings to light concerns over future warmings possible impacts on alpine species distribution and speciation, underlining the urgency for increased conservation efforts. C_LI

evolutionary biology↗

bioRxiv2023

MultiPPIMI: a multimodal deep learning framework for predicting interactions between protein-protein interaction targets and modulators

Protein-protein interactions (PPIs) are essential for various biological processes and diseases. However, most existing computational methods for identifying PPI modulators require either target structure or reference modulators, which restricts their applicability to novel PPI targets. To address this challenge, we propose MultiPPIMI, a sequence-based deep learning framework that predicts the interaction between any given PPI target and modulator. MultiPPIMI integrates multimodal representations of PPI targets and modulators, and uses a bilinear attention network to capture inter-molecular interactions. Experimental results on our curated benchmark dataset show that MultiPPIMI achieves an average AUROC of 0.837 in three cold-start scenarios, and an AUROC of 0.994 in the random-split scenario. Furthermore, the case study show that MultiPPIMI can assist molecular simulations in screening inhibitors of Keap1/Nrf2 PPI interactions. We believe that the proposed method provides a promising way to screen PPI-targeted modulators.

bioinformatics↗

bioRxiv2023

DHX36 binding induces RNA structurome remolding and regulates RNA abundance via m6A/YTHDF1

RNA structure constitutes a new layer of gene regulatory mechanisms. RNA binding proteins can modulate RNA secondary structures, thus participating in post-transcriptional regulation. The DEAH-box helicase 36 (DHX36) is known to bind and unwind RNA G-quadruplex (rG4) structure but the transcriptome-wide RNA structure remodeling induced by DHX36 binding and the impact on RNA fate remain poorly understood. Here, we investigate the RNA structurome alteration induced by DHX36 depletion. Our findings reveal that DHX36 binding induces structure remodeling not only at the localized binding sites but also on the entire mRNA transcript most pronounced in3UTR regions. DHX36 binding increase structural accessibility at 3UTRs which is correlated with decreased post-transcriptional mRNA abundance. Further analyses and experiments uncover that DHX36 binding sites are enriched for N6-methyladenosine (m6A) modification and YTHDF1 binding; and DHX36 induced structural change may facilitate YTHDF1 binding to m6A sites leading to RNA degradation. Altogether, our findings uncover the structural remodeling effect of DHX36 binding and its impact on RNA abundance through regulating m6A dependent YTHDF1 binding.

molecular biology↗

bioRxiv2023

Stimulation of mRNA translation rescues hippocampal synaptic plasticity and memory in mouse models of Alzheimer's disease

Impaired synaptic plasticity and progressive memory deficits are major hallmarks of Alzheimers disease (AD). Hippocampal mRNA translation, required for memory consolidation, is defective in AD. Here, we show that systemic treatment with (2R,6R)- hydroxynorketamine (HNK), an active metabolite of the antidepressant ketamine, prevented deficits in hippocampal mRNA translation, long-term potentiation (LTP) and memory induced by AD-linked amyloid-{beta} oligomers (A{beta}Os) in mice. HNK activated hippocampal extracellular signal-regulated kinase 1/2 (ERK1/2), mechanistic target of rapamycin (mTOR), and p70S6 kinase 1 (S6K1)/ribosomal protein S6 (S6), which promote protein synthesis and synaptic plasticity. Stimulation of S6 phosphorylation by HNK was mTORC1-dependent, while rescue of hippocampal LTP and memory in HNK-treated A{beta}O-infused mice was ERK1/2-dependent and, partially, mTORC1- dependent. Remarkably, treatment with HNK corrected LTP and memory deficits in aged APP/PS1 mice. Transcriptomic analysis further showed that HNK rescued signaling pathways that are aberrant in APP/PS1 mice, including inflammatory and hormonal responses, and programmed cell death. Taken together, our findings demonstrate that HNK induces signaling and transcriptional responses that correct deficits in hippocampal synaptic plasticity and memory in AD mouse models. These results raise the prospect that HNK could serve as a therapeutic to prevent or reverse memory decline in AD.

neuroscience↗

bioRxiv2023

High-throughput and genome-scale targeted mutagenesis using CRISPR in a non-model multicellular organism, Bombyx mori

Large-scale genetic mutant libraries are powerful approaches to interrogating genotype-phenotype correlations and identifying genes responsible for certain environmental stimuli, both of which are the central goal of life science study. We produced the first large-scale CRISPR/Cas9-induced library in a non-model multicellular organism, Bombyx mori. We developed a piggyBac-delivered binary genome editing strategy, which can simultaneously meet the requirements of mixed microinjection, efficient multi-purpose genetic operation, and preservation of growth-defect lines. We constructed a single-guide RNA (sgRNA) plasmid library containing 92,917 sgRNAs targeting promoters and exons of 14,645 protein-coding genes, established 1726 transgenic sgRNA lines following microinjection of 66,650 embryos, and generated 300 mutant lines with diverse phenotypic changes. Phenomic characterization of mutant lines identified a large set of genes responsible for visual phenotypic or economically valuable trait changes. Next, we performed pooled context-specific positive screens for tolerance to environmental pollute cadmium exposure, and identified KWMTBOMO12902 as a strong candidate gene for breeding applications in sericulture industry. Collectively, our results provide a novel and versatile approach for functional B. mori genomics, and a powerful resource for identifying key candidate genes potential for improving various economic traits. This study also demonstrates the effectiveness, practicality, and convenience of large-scale mutant libraries in other non-model organisms.

genomics↗

bioRxiv2023

Collective dynamics of formin and microtubule and its crosstalk mediated by FHDC1

The coordination between actin and microtubule network is crucial, yet our understanding of the underlying mechanisms remains limited. In this study, we used travelling waves in the cell cortex to characterize the collective dynamics of cytoskeletal networks. Our findings show that Cdc42 and F-BAR-dependent actin waves in mast cells are mainly driven by formin-mediated actin polymerization, with the microtubule-binding formin FH2 domain-containing protein 1 (FHDC1) identified as an early regulator. The depolymerization of microtubules coincides with the nucleation of actin waves, and the concurrent release of FHDC1 from microtubule is required for actin waves. Lastly, we show the importance of the actin-microtubule linkage mediated by FHDC1 in crucial cellular processes such as cell division and migration. Our data provided molecular insights into the nucleation mechanisms of actin waves and uncover an antagonistic interplay between microtubule and actin polymerization in their collective dynamics.

cell biology↗

bioRxiv2023

Shape-changing electrode array for minimally invasive large-scale intracranial brain activity mapping

Large-scale brain activity mapping is important for understanding the neural basis of behaviour. Electrocorticograms (ECoGs) have high spatiotemporal resolution, bandwidth, and signal quality. However, the invasiveness and surgical risks of electrode array implantation limit its application scope. We developed an ultrathin, flexible shape-changing electrode array (SCEA) for large-scale ECoG mapping with minimal invasiveness. SCEAs were inserted into cortical surfaces in compressed states through small openings in the skull or dura and fully expanded to cover large cortical areas. MRI and histological studies on rats proved the minimal invasiveness of the implantation process and the high chronic biocompatibility of the SCEAs. High-quality micro-ECoG activities mapped with SCEAs from rodent brains during seizures and canine brains during the emergence period revealed the spatiotemporal organization of different brain states with resolution and bandwidth that cannot be achieved using existing noninvasive techniques. The biocompatibility and ability to map large-scale physiological and pathological cortical activities with high spatiotemporal resolution, bandwidth, and signal quality in a minimally invasive manner offer SCEAs as a superior tool for applications ranging from fundamental brain research to brain-machine interfaces.

neuroscience↗