Biology subjects

Huang, S.

Publications and source records attributed to Huang, S..

At least 145 records · Page 8Linked to original sources

bioRxiv2024

Birthdate aligns vestibular sensory neurons with central and motor partners across a sensorimotor reflex circuit for gaze stabilization

Developing populations of connected neurons often share spatial and/or temporal features that anticipate their assembly. A unifying spatiotemporal motif might link sensory, central, and motor populations that comprise an entire circuit. In the sensorimotor reflex circuit that stabilizes vertebrate gaze, central and motor partners are paired in time (birthdate) and space (dorso-ventral). To determine if birthdate and/or dorso-ventral organiza-tion could align the entire circuit, we measured the spatial and temporal development of the sensory circuit node: the vestibular ganglion neurons. We discovered that progressive dorsal-to-ventral organization closely predicts vestibular ganglion development, with additional organization along its functional (rostrocaudal) axis. With an acute optical lesion and calcium imaging paradigm, we found that this common spatiotemporal axis anticipated functional sensory-to-central partner matching. We propose a "first-come, first-served" model in which birth-date organizes and assembles the sensory, central, and motor populations that comprise the gaze stabilization circuit, a general strategy for poly-synaptic circuit assembly across embryonically-diverse neural populations. SUMMARY STATEMENTCircuit nodes often develop along common axes. We find that a "first-come, first-served" temporal rule underscores the organization of a canonical sensorimotor circuit for gaze stabilization, simplifying poly-synaptic assembly.

neuroscience↗

bioRxiv2024

Structural and Mechanistic Insights into Symmetry Conversion in Plant GORK K+ Channel Regulation

GORK is a shaker-like potassium channel in plants that contains ankyrin (ANK) repeats. In guard cells, activation of GORK causes K+ efflux, reducing turgor pressure and closing stomata. However, how GORK is regulated remains largely elusive. Here, we solved the cryo-EM structure of Arabidopsis GORK, revealing an unusual symmetry reduction (from C4 to C2) feature within its tetrameric assembly. This symmetry reduction in GORK channel is driven by ANK dimerization, which disrupts the coupling between transmembrane helices and cytoplasmic domains, thus maintaining GORK in an autoinhibited state. Electrophysiological and structural analyses further confirmed that ANK dimerization inhibits GORK, and its removal restores C4 symmetry, converting GORK to an activatable state. This dynamic switching between C2 and C4 symmetry, mediated by ANK dimerization, presents a GORK target site that guard cells regulate to switch the plant K+ channel between inhibited and activatable states, thus controlling stomatal movement in response to environmental stimuli.

plant biology↗

bioRxiv2024

Reprogramming the genome of M13 bacteriophage for all-in-one personalized cancer vaccine

Peptide-based vaccines face limitations in immunogenicity and stability, and challenges in co-delivering antigens and adjuvants effectively. Virus-based nanoparticles, particularly M13 bacteriophage, present a promising solution due to their genetic modifiability, intrinsic adjuvanticity, and efficient antigen presentation capabilities. Here we developed a programmable M13 phage-based personalized cancer vaccine enabling single-step antigen-adjuvant assembly. Specifically, we designed a reprogrammed (RP) phage platform that precisely regulates Toll-like receptor 9 activation by programming its genome sequence and modulates antigen density through genetic engineering. Vaccination studies with RP phages demonstrated that the immune response could be modulated by fine-tuning the adjuvanticity and antigen density, revealing an optimal antigen dose and adjuvanticity for maximum vaccine efficacy. The RP phage induced a remarkable 24-fold increase in neoantigen-specific CD8+ T cells and eradicated established MC-38 tumors when combined with anti-PD-1 therapy. These findings highlight the RP phages potential as a powerful nanovaccine platform for personalized cancer vaccines.

bioengineering↗

bioRxiv2024

Understanding the Dynamics of Biomass Deconstruction by the Cellulolytic Anaerobe C. thermocellum

Clostridium thermocellum is one of the most efficient microorganisms for the deconstruction of cellulosic biomass. To achieve this high level of cellulolytic activity, C. thermocellum uses large multienzyme complexes known as cellulosomes to break down complex polysaccharides, notably cellulose, found in plant cell walls. The attachment of bacterial cells to the nearby substrate via the cellulosome has been hypothesized to be the reason for this high efficiency. The region lying between the cell and the substrate has shown great variation and dynamics that are affected by the growth stage of cells and the biomass used for growth. Here, we utilized both photoactivation localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM) in combination with Density-Based Spatial Clustering of Applications with Noise (DBSCAN) to study the distribution of C. thermocellum cellulosomes at different stages of growth when actively growing on soluble and insoluble substrates, providing a clearer picture of the dynamics of cellulosome populations at the enzyme microbe substrate interface. This research demonstrates the promising application of novel optical methodologies in tandem with targeted mutations within C. thermocellum to test the prevailing theories regarding the mechanisms of cellulosomes and their potential to shuttle onto the biomass for the attachment of C. thermocellum to improve biomass deconstruction.

microbiology↗

bioRxiv2024

Machine learning engineered PoLixNano nanoparticles overcome delivery barriers for nebulized mRNA therapeutics

There continues to be a dearth of competent inhalable mRNA delivery although it holds great potential for addressing a wide variety of refractory diseases. The huge advances seen with parenteral-administered lipid nanoparticle (LNP) have not been translated into nebulized mRNA delivery due to the aggressive nebulization process and insurmountable barriers inherent to respiratory mucosa. Here, we show amphiphilic block copolymers revealed by machine learning (ML) can spontaneously form stabilized nanoparticles (PoLixNano) with the lipids components of LNP and simultaneously impart the PoLixNano with "shield" (shear force-resistant) and "spear" (pulmonary barriers-penetrating abilities) capabilities. We present a ML approach that leverages physicochemical properties and inhaled mRNA transfection profiles of a chemically diverse library of polymeric components to validate the integration of "shield" and "spear" properties as highly predictive indicators of transfection efficiency. This quantitative structure-mRNA transfection prediction (QSMTP) model identifies top-performing amphiphilic-copolymers from more than 10000 candidates and suggests their mucus-penetrating ability outweights the shear force-resistant property in contributing to efficient mRNA transfection. The optimized PoLixNano substantially outperforms the LNP counterpart and mediates up to 1114-times higher levels of mRNA transfection in animal models with negligible toxicities. The PoLixNano promotes overwhelming SARS-CoV-2 antigen-specific sIgA antibody secretion and expansion of TRM cells which collectively confers 100% protection in mice against lethal SARS-CoV-2 challenges and blocks the transmission of Omicron variant between hamsters. PoLixNano also displays versatile therapeutic potential in lung carcinoma and cystic fibrosis models. Our study provides new insights for designing delivery platforms of aerosol-inhaled mRNA therapeutics with clinical translation potential.

synthetic biology↗

bioRxiv2024

Long-term Immunity of a Microneedle Array Patch of SARS-CoV-2 S1 Protein Subunit Vaccine Irradiated by Gamma Rays in Mice

COVID-19 vaccines effectively prevent symptomatic infection and severe disease, including hospitalization and death. However, unequal vaccine distribution during the pandemic, especially in low- and middle-income countries, has led to the emergence of vaccine-resistant strains. This underscores the need for alternative, safe, and thermostable vaccine platforms, such as dissolved microneedle array patches (MAP) delivering a subunit vaccine, which eliminate the need for cold chain and trained healthcare personnel. This study demonstrates that the SARS-CoV-2 S1 monomer with RS09, a TLR-4 agonist peptide, serves as an optimal protein subunit immunogen. This combination stimulates a stronger S1-specific immune response, resulting in binding to the membrane-bound spike on the cell surface and ACE2-binding inhibition, compared to the monomer S1 alone or trimer S1, regardless of RS09. MAP delivery of the rS1RS09 subunit vaccine elicited higher and longer-lasting immunity compared to conventional intramuscular injection. S1-specific IgG levels remained significantly elevated for up to 70 weeks post-administration. Additionally, different doses of 5, 15, and 45 g of MAP vaccines induced robust and sustained Th2-prevalent immune responses, suggesting a dose-sparing effect and inducing significantly high neutralizing antibodies against the Wuhan, Delta, and Omicron variants at 15 and 45 g dose. Moreover, gamma irradiation as a terminal sterilization method did not significantly affect immunogenicity, with irradiated vaccines maintaining comparable efficacy to non-irradiated ones. The stability of MAP vaccines was evaluated after long-term storage at room temperature and refrigeration for 19 months, showing minimal protein degradation. Further, after an additional one-month of storage at elevated temperature (42{degrees}C), rS1RS09 in both non-irradiated and irradiated MAP degraded less than 3%, while the liquid subunit vaccine degraded over 23%. Overall, these results indicate that gamma irradiation sterilized MAP-rS1RS09 vaccines maintain stability during extended storage without refrigeration, supporting their potential for mass production and widespread use in global vaccination efforts.

microbiology↗

bioRxiv2024

Coma pattern-based autofocusing unlocks superior performance in unravelling single-cell dynamics during bacterial cold shock response

Imaging-based single-cell physiological profiling holds great potential for uncovering fundamental bacterial cold shock response (CSR) mechanisms, but its application is impeded by severe focus drift during rapid temperature downshifts required for CSR induction. Here, we introduce LUNA (Locking Under Nanoscale Accuracy), an innovative autofocusing method that leverages the coma pattern of detection light to characterize focus drift. LUNA improves the focusing precision down to 3 nm and extends the focusing range to at least 40 times the objective depth-of-focus. These advancements enable us to investigate the complete dynamics of bacterial single-cell CSR, revealing continuous cellular growth and division. We resolve a three-phase adaptation process characterized by distinct growth deceleration dynamics, and show that bacterial cells maintain robust size regulation and coordinate uniform adaptation to cold shock through synchronized growth and elapsed cycles. Notably, a model based on scattering theory reconciles the paradox between the growth lag of batch culture and continuous single-cell growth. These findings fundamentally transform our understanding of bacterial CSR and highlight LUNAs excellent potential for expanding state-of-the-art research in biology.

microbiology↗

bioRxiv2024

Strong segregation promotes self-destructive cooperation

Self-destructive cooperator (SDC), where individuals sacrifice themselves for others, poses significant personal costs yet is widespread in nature. Traditional group selection theory struggles to explain its persistence, as the extreme cost of self-destruction typically exceeds the benefit to these individuals. Here, we predict that this behavior can endure in structured environments with strong segregation, where populations are divided into homogenous groups originating from one or two founding members. In such contexts, the benefits derived from SDC are primarily confined within the homogenous SDC groups, thus preserving the value of this altruistic sacrifice and ensuring its maintenance. To validate our hypothesis, we employ a synthetic system with engineered bacteria to mimic both SDC and non-sacrificing cheaters. We then conduct automated experiments facilitated by biofoundry technology to monitor and operate the subgroups with diverse growth behaviors stemming from a restricted number of initial cells because of strong segregation. Eventually, we demonstrate that SDC indeed maintains under strong segregation, and high stress benefits SDC because it reduces the benefits received by cheaters in heterogenous subgroups. This study extends the group selection theory to encompass even the most extreme manifestations of altruism and highlights the potential of automation in evolutionary research.

microbiology↗

bioRxiv2024

mRNA expression is co-regulated by non-nucleolar RNA polymerase I

The relationship between gene transcription and chromatin organization is an area of active study. Due to its role in mRNA synthesis, many studies have focused on the regulaton of RNA polymerase II (Pol-II) function by supranucleosomal structure and vice-versa. In contrast, there is little work on the function of RNA polymerase I (Pol-I) in non-nucleolar chromatin. Prior work has shown that Pol-I engages with components of Pol-II on rDNA, but its role in global transcription and chromatin structure beyond the nucleolus has largely been ignored. By pairing auxin-inducible degron technology with nanoscopic imaging, RNA-Seq, and Hi-C, we found that Pol-I and Pol-II co-regulate conformationally defined chromatin domains and mRNA synthesis. Mechanistically, Pol-I maintains the positioning of intronic and intergenic chromatin within domains for the proper expression of exon elements. Consequently, Pol-I loss disrupts genome connectivity, in situ chromatin domains, and the expression of mRNA, genome-wide.

genomics↗

bioRxiv2024

Semantic Dimensions Support the Cortical Representation of Object Memorability

Recent work in vision sciences contends that objects carry an intrinsic property, memorability, that describes the likelihood that an object can be successfully encoded and later retrieved from memory. It has been shown that object memorability is supported by semantic information, but the neural correlates involved are largely unexplored. The present study explores these premises and asks whether neural correlates of object memorability can be accounted for by semantic dimensions. To investigate these questions, we combine three datasets: (1) feature norms for a database of [~]1000 natural object images, (2) normative conceptual and perceptual memory data for those objects, and (3) neuroimaging data from an fMRI study collected using a subset (n=360) of those objects. We found that object-wise memorability elicits consistent brain activation across participants in key mnemonic regions (e.g., hippocampus and rhinal cortex), and that a substantial portion of the variance in this brain activity is mediated by the semantic factors describing these images. Regions with the strongest mediation effects are associated with sensory, motor, and visual processes, suggesting that the relationship between memorability and semantics may align with a sensory-functional account of the representation of concepts in the brain.

neuroscience↗

bioRxiv2024

Cell extract-based in vitro DNA replication enables sustainable cell-free gene expression

Cell extract-based cell-free gene expression (CFE) systems break cellular boundaries and create emerging platforms for synthetic biology applications. However, these systems lack intrinsic DNA replication capability, thereby limiting sustained transcription and translation in a cell-free environment. Here, we introduce a LoopReX system based on E. coli CFE by integration of the DNA replication machinery, enabling iterative in vitro DNA replication and sustainable cell-free gene expression. We establish LoopReX by integrating phi29 DNA polymerase into the crude lysate-based E. coli CFE system, allowing for coupled DNA replication and protein expression. We elucidate the synergetic mechanisms between T7 RNA polymerase and phi29 DNA polymerase in facilitating in vitro DNA replication. Additionally, we optimize LoopReX reaction conditions by machine learning strategies. Finally, we demonstrate that the enhanced LoopReX system achieves highly efficient DNA replication and protein production in an iterative, scalable, and sustainable manner. We anticipate that LoopReX will significantly advance the application of CFE in synthetic biology.

synthetic biology↗

bioRxiv2024

Family-Wide Photoproximity Profiling of Integrin Protein Social Networks in Cancer

Integrin family transmembrane receptors mediate dynamic interactions between cells and their extracellular microenvironment. The heterogeneous interaction partners of integrins directly regulate cell adhesion, motility, proliferation, and intracellular signaling. Despite the recognized importance of protein-protein interactions and the formation of signaling hubs around integrins, the ability to detect and quantify these dynamic binding partners with high spatial and temporal resolution remains challenging. Here, we developed an integrin-family-directed quantitative photoproximity protein interaction (PhotoPPI) profiling method to detect and quantify native integrin-centered protein social networks on live cells and tissues without the need for genetic manipulation, antibodies, or non-physiologic cell culture conditions. We drafted quantitative maps of integrin-centered protein social networks, highlighting conserved and unique binding partners between different cell types and cellular microenvironments. Comparison of integrin social networks in cancer cell lines of diverse tissue of origin and disease state identified specific AND-gate binding partners involved cell migration, microenvironmental interactions and proliferation that serve as markers of tumor cell metastatic state. Finally, we identified unique combinations - or barcodes - of integrin-proximal proteins on the surface of pre- and post-metastatic triple negative breast cancer (TNBC) cells whose expression strongly correlate with both positive and negative disease progression and outcomes in TNBC patients. Taken together, these data provide the first family-wide high-resolution maps of native protein interactors on live cells and identify dynamic integrin-centered social networks as potential AND-gate markers of cell identity, microenvironmental context and disease state.

cancer biology↗

bioRxiv2024

Cortico-hippocampal interactions underlie schema-supported memory encoding in older adults

Although episodic memory is typically impaired in older adults (OAs) compared to young adults (YAs), this deficit is attenuated when OAs can leverage their rich semantic knowledge, such as their knowledge of schemas. Memory is better for items consistent with pre-existing schemas and this effect is larger in OAs. Neuroimaging studies have associated schema use with the ventromedial prefrontal cortex (vmPFC) and hippocampus (HPC), but most of this research has been limited to YAs. This fMRI study investigated the neural mechanisms underlying how schemas boost episodic memory in OAs. Participants encoded scene-object pairs with varying congruency, and memory for the objects was tested the following day. Congruency with schemas enhanced object memory for YAs and, more substantially, for OAs. FMRI analyses examined how cortical modulation of HPC predicted subsequent memory. Congruency-related vmPFC modulation of left HPC enhanced subsequent memory in both age groups, while congruency-related modulation from angular gyrus (AG) boosted subsequent memory only in OAs. Individual differences in cortico-hippocampal modulations indicated that OAs preferentially used their semantic knowledge to facilitate encoding via an AG-HPC interaction, suggesting a compensatory mechanism. Collectively, our findings illustrate age-related differences in how schemas influence episodic memory encoding via distinct routes of cortico-hippocampal interactions.

neuroscience↗

bioRxiv2024

Interpretable high-resolution dimension reduction of spatial transcriptomics data by DeepFuseNMF

Spatial transcriptomics (ST) technologies have revolutionized tissue architecture studies by capturing gene expression with spatial context. However, high-dimensional ST data often have limited spatial resolution and exhibit considerable noise and sparsity, posing significant challenges in deciphering subtle spatial structures and underlying biological activities. Here, we introduce SpaHDmap, an interpretable dimension reduction framework that enhances spatial resolution by integrating ST gene expression with high-resolution histology images. SpaHDmap incorporates non-negative matrix factorization into a multimodal fusion encoder-decoder architecture, enabling the identification of interpretable, high-resolution embeddings. Furthermore, SpaHDmap can simultaneously analyze multiple samples and is compatible with various types of histology images. Extensive evaluations on synthetic and real ST datasets from various technologies and tissue types demonstrate that SpaHDmap can effectively produce highly interpretable, high-resolution embeddings, and detects refined spatial structures. SpaHDmap represents a powerful approach for integrating ST data and histology images, offering deeper insights into complex tissue structures and functions.

bioinformatics↗

bioRxiv2024

Decoding Specificity of Cyanobacterial MysDs in Mycosporine-Like Amino Acid Biosynthesis through Heterologous Expression in Saccharomyces cerevisiae

Mycosporine-like amino acids (MAAs) are potent natural UV-protectants, but their industrial production is hindered by efficiency and sustainability issues of large-scale extraction of their native hosts. Heterologous expression of MAA biosynthesis pathway genes in chassis organisms provides a promising alternative route, though the substrate promiscuity of the ATP-grasp ligase MysD complicates the biosynthesis of specific MAAs. In this study, we developed a Saccharomyces cerevisiae strain with enhanced capacity of producing mycosporine-glycine (MG), through genomic expression of biosynthesis pathway genes and knockout of competing pathway genes. This strain serves as an efficient MysD expression platform, which converts MG into shinorine and porphyra-334. Through structural modelling, site-directed mutagenesis and mutant characterization, we identified two residues on the omega-loop of MysD involved in determining product specificity. We further characterized the product specificity of 20 MysDs from diverse cyanobacterial lineages and confirmed the residue pattern-product specificity correlation. Our findings provide guidance for screening, selecting, and designing novel MysDs for industrial-scale MAA production through heterologous expression.

synthetic biology↗

bioRxiv2024

ERVcancer: a web resource designed for querying activation of human endogenous retroviruses across major cancer types

Human endogenous retroviruses (HERVs) compose approximately 8% of the human genome, co-opted into the dynamic regulatory network of cellular potency in early embryonic development. In recent studies, resurgent HERVs transcriptional activity has been frequently observed in many types of human cancers, suggesting their potential functions in the occurrence and progression of malignancy. However, a web resource dedicated to querying the relationship between activation of HERVs and cancer development is lacking. Here, we have constructed a database to explore the sequence information, expression profiles, survival prognosis, and genetic interactions of HERVs in diverse cancer types. Our database currently incorporates RNA sequencing (RNA-seq) data of 580 HERVs across 16246 samples, comprising 151 early embryonic data from the Gene Expression Omnibus (GEO) database, 8051 human adult tissues data from the Genotype-Tissue Expression (GTEx) project, 932 cancer cell lines data from the Cancer Cell Line Encyclopedia (CCLE) project, 6478 tumoral and 634 normal tissue samples data from The Cancer Genome Atlas (TCGA) project. The primary goal is to provide an easily accessible and user-friendly database for professionals in the fields of bioinformatics, pathology, pharmacology, and related areas, enabling them to efficiently screen the activity of HERVs of interest in normal and cancerous tissues and evaluate the clinical relevance. The ERVcancer database is available at http://kyuanlab.com/ervcancer/.

genomics↗

bioRxiv2024

MagnoliidsGDB：An integrated functional genomics database for Magnoliids

In this study, we present MagnoliidsGDB, an integrated functional genomics database specifically developed for magnoliids, a group of plants known for their unique characteristics and medicinal properties. As of March 2024, MagnoliidsGDB has collected 31 genome sequences from 24 species, 149 resequencing datastes from 4 species, 842 transcriptomic datasets from 20 species, and metabolomic data from 15 species. This comprehensive resource allows researchers to explore the genomic, transcriptomic, and metabolomic variations of magnoliids. The user-friendly search and analysis functionalities of MagnoliidsGDB facilitate the study of genomic variations, gene functions, plant evolution and key metabolites of magnoliids. We hope this database will contribute to the study of magnoliids and increase our understanding of the origin, variation, and molecular basis of the unique biological features of magnoliids.

evolutionary biology↗

bioRxiv2024

Improving the value utilization of tuna peptide powder for the cosmetics field through ozone oxidation

To improve the utilization efficiency of small molecule peptides in marine proteins and promote their application in cosmetics, this study adopts ozone oxidation to conduct deodorization research on tuna small molecule peptides. To devise a method for the ozone oxidation and deodorization of tuna peptide powder suitable for the cosmetics field, orthogonal tests were carried out. The time, ozone concentration, and temperature were adjusted to determine the optimal conditions for ozonation and deodorization of tuna peptide powder. The results showed that at 50{degrees}C and an ozone concentration of 99.10 x 103 mg/m3, wet ozone oxidation for 40 min can also significantly reduce the fishy smell. Under these conditions, the color of tuna peptide powder treated with wet ozone was lighter. In addition, the main volatile compounds were detected by gas chromatography-mass spectrometry (GC-MS). The content of the main fishy volatile substance, hexanal, decreased by 66.4%, and two octyl aldehydes were observed. The results also showed that the protein activity of tuna peptide powder after ozonation remained unchanged. Thus, this study presents an approach to the ozone oxidation of tuna peptide powder that is suitable for cosmetics.

bioengineering↗