Biology subjects

Shen, Q.

Publications and source records attributed to Shen, Q..

At least 55 records · Page 3Linked to original sources

bioRxiv2024

Evidence of Silencing of Intestinal Inflammatory and Immune Transcripts Following Induction of Joint Inflammation

Disrupted intestinal epithelial barrier function has been proposed to be integral to rheumatoid arthritis (RA) progression and pathogenesis. To further define the molecular pathways in synovial inflammation and the response of the intestinal tissues, we have used a rat model of mono-joint inflammatory arthritis, induced by intra-articular injection of Complete Freunds adjuvant (CFA). The predominant inflammatory response of a single injection of the adjuvant into the knee joint resulted in rapid and reproducible formation of a fibrotic myeloid-infiltrated synovial pannus. Our aim was to determine how intestinal tissues, including the proximal and distal ileum and distal colon, responded to inflammatory changes in the synovium in a temporally coordinated manner by comparing their transcriptomic landscapes using RNASeq analyses. We confirmed the timeline of joint inflammation by knee joint swelling measurement, increased synovial fluid levels of bikunin (a component of both the acute phase protein pre-alpha-inhibitor and inter-alpha-inhibitor) and demonstrated a self-correcting response of trabecular and cortical bone to the CFA challenge. Intestine-specific responses were monitored by 16S microbiome amplicon sequencing, histopathology for mucus layer integrity, and immune cell immunohistochemistry. We present data that shows the intestinal tissue displays an allostatic response to the acute joint inflammation and was region specific. The ileum primarily responded with increased mucus secretion and silencing of T-cell specific pathways, whereas the colon showed a transient upregulation of macrophages, with a broader suppression of immune related and metabolic pathway related transcripts. Interestingly, many neuropathways were activated early but then suppressed later in both the ileum and colon. There were only insignificant changes in the fecal microbiome composition in ileum or colon post-CFA administration. In summary, our data show for the first time a suppression of intestinal inflammatory and immune responses following the induction of joint inflammation and only minimal and transient changes in the microbiome. The results help clarify the molecular responses of intestinal tissues to inflammatory stresses that accompany the pathogenesis of inflammatory joint diseases.

cell biology↗

bioRxiv2024

Experimental method for creating skin with acquired appendage dysfunction

Mammalian skin appendages, such as hair follicles and sweat glands, are essential for both esthetic and functional purposes. Conditions such as burns and ulcers can lead to dysfunction or loss of skin appendages and result in hair loss and dry skin, posing challenges in their regeneration. Existing animal models are insufficient for studying acquired dysfunction of skin appendages without underlying genetic causes. This study aimed to develop more clinically relevant mouse models by evaluating two approaches: keratinocyte transplantation and grafting of skin at varying thicknesses. GFP-expressing keratinocytes were transplanted into ulcers on nude mice, leading to re-epithelialization with minimal skin appendages at 4 weeks after transplantation. However, the re-epithelialized area was largely derived from recipient cells, with the grafted cells contributing to only 1.31% of the area. In the skin grafting model, donor skin from GFP transgenic mice was grafted onto nude mice at three thicknesses: full thickness, 10/1000 inch, and 5/1000 inch. The grafted area of the 5/1000-inch grafts remained stable at 89.5% of its original size 5 weeks after transplantation, ensuring a sufficiently large skin area. The 5/1000-inch grafts resulted in a significant reduction in skin appendages, with a mean of only 3.73 hair follicles per 5 mm, compared with 69.7 in the control group. The 5/1000-inch skin grafting in orthotopic autologous transplantation also showed the achievement of skin surfaces with a minimal number of skin appendages. Therefore, a mouse model with skin grafting demonstrated stability in producing large areas of skin with minimal appendages. In conclusion, these two models with acquired skin appendage dysfunction and no underlying genetic causes provide valuable tools for researching skin appendage regeneration, offering insights into potential therapeutic strategies for conditions involving skin appendage loss.

bioengineering↗

bioRxiv2024

Motion correction with subspace-based self-navigation for combined angiography, perfusion and structural imaging

Motion artifacts are problematic in many MRI modalities. "Self-navigating" approaches are desirable, since no additional scan time or hardware is required. However, the generation of a navigator image, to estimate and correct motion, is difficult in cases where the tissue contrast is changing during the navigator acquisition window, such as in magnetization- prepared methods. Here we propose a subspace approach to reconstruct accurate navigators in the presence of time-varying tissue contrast and apply it to a combined angiography, perfusion and structural imaging method using a golden ratio 3D cones trajectory. This arterial spin labeling-based pulse sequence relies on subtraction of label and control images to isolate the relatively weak blood signal, making it particularly susceptible to motion corruption. An inversion pulse leads to time-varying tissue contrast across the readout train, but by reconstructing subspace coefficient maps directly, artifacts due to the varying contrast were alleviated. This resulted in high-quality navigator images that were subsequently registered to estimate and correct for motion. In addition, a split-update method was proposed to efficiently reconstruct from mismatched label/control k-space data with locally low rank regularization enforced on the difference image. The correction process was tested with numerical simulation and in vivo data from 8 healthy subjects with and without cued motion. In numerical simulation, the subspace- based navigator achieved an 84% reduction in RMSE of residual motion compared to without motion correction. In vivo, motion correction resulted in noise-like and background artifacts being greatly reduced and vessel sharpness being noticeably improved. Correlation of angiography, perfusion and structural images with motion-free reference images also increased by 159%, 53% and 12%, respectively, after motion correction. These results show that subspace-based navigators can effectively improve the motion robustness of MR imaging in contrast-varying acquisitions.

neuroscience↗

bioRxiv2024

Interspecies interaction reshapes the fitness landscape of evolved genotypes

Microbial interaction and their evolution is vital for shaping the structure and function of microbial communities. However, the mechanisms governing the directionality and stability of the evolution of interactions within microbial communities remain poorly understood. Here, we used a syntrophic two-species biofilm consortium composed of Bacillus velezensis SQR9 and Pseudomonas stutzeri XL272 that promotes plant growth through their metabolic interactions and investigated how the interactions within the consortium change over evolutionary timescale to characterize the phenotypic and genetic diversification. The focal species B. velezensis SQR9 rapidly diversified into diverse colony morphotypes, both in the presence and absence of its interactor, P. stutzeri XL272, with variable frequencies. These morphotypes displayed phenotypic differentiation among biofilm formation, planktonic growth, and spore formation. The evolved P. stutzeri altered the fitness landscape of B. velezensis morphotypes, allowing the weaker rough morphotype to outcompete the biofilm-enhanced slimy morphotype. Whole genome re-sequencing correlated these phenotypic changes with mutations in specific genes encoding regulators of B. velezensis, including ywcC, comA, comP, degS, degQ and spo0F. The coevolutionary partner, P. stutzeri increased its exopolysaccharide production that could be explained by a frame shift mutation in cpsA gene encoding capsular polysaccharide (CPS) biosynthesis protein. Compared with the mono-evolution, co-evolved B. velezensis populations showed greater mutation accumulation in intergenic regions, which led to greater genetic parallelism. Furthermore, the dissimilarity between mono-evolved and co-evolved populations increased over time. Our study reveals intricate genetic diversification and fitness differentiation within a biofilm consortium, shaped by both abiotic conditions and biotic interactions.

microbiology↗

bioRxiv2024

Ultra-high temporal resolution 4D angiography using arterial spin labeling with subspace reconstruction

PurposeTo achieve ultra-high temporal resolution non-contrast 4D angiography with improved spatiotemporal fidelity. MethodsContinuous data acquisition using 3D golden-angle sampling following an arterial spin labeling preparation allows for flexibly reconstructing 4D dynamic angiograms at arbitrary temporal resolutions. However, k-space data is often temporally "binned" before image reconstruction, negatively affecting spatiotemporal fidelity and limiting temporal resolution. In this work, a subspace was extracted by linearly compressing a dictionary constructed from simulated curves of an angiographic kinetic model. The subspace was used to represent and reconstruct the voxelwise signal timecourse at the same temporal resolution as the data acquisition without temporal binning. Physiological parameters were estimated from the resulting images using a Bayesian fitting approach. A group of 8 healthy subjects were scanned and the in-vivo results reconstructed by different methods were compared. Due to the difficulty of obtaining ground truth 4D angiograms with ultra-high temporal resolution, the in-vivo results were cross-validated with numerical simulations. ResultsThe proposed method enables 4D time-resolved angiography with much higher temporal resolution (14.7 ms) than previously reported ([~]50 ms) whilst maintaining high spatial resolution (1.1 mm isotropic). Blood flow dynamics were depicted in greater detail, thin vessel visibility was improved, and the estimated physiological parameters also exhibited more realistic spatial patterns with the proposed method. ConclusionIncorporating a subspace compressed kinetic model into the reconstruction of 4D ASL angiograms notably improved the temporal resolution and spatiotemporal fidelity, which was subsequently beneficial for accurate physiological modeling.

neuroscience↗

bioRxiv2024

Bridging the Gap: biofilm-mediated establishment of Bacillus velezensis on Trichoderma guizhouense mycelia

Bacterial-fungal interactions (BFIs) are important in ecosystem dynamics, especially within the soil rhizosphere. The bacterium Bacillus velezensis SQR9 and the fungus Trichoderma guizhouense NJAU 4742 have garnered considerable attention due to their roles in promoting plant growth and protecting their host against pathogens. In this study, we utilized these two model microorganisms to investigate BFI. We firstly demonstrate that while co-inoculation of B. velezensis and T. guizhouense could promote tomato growth, these two microorganisms display mutual antagonism on agar solidified medium. To resolve this contradiction, we developed an inoculation method, that allows B. velezensis colonization of T. guizhouense hyphae and performed a transcriptome analysis. During colonization of the fungal hyphae, B. velezensis SQR9 upregulates expression of biofilm related genes (e.g. eps, tasA, and bslA) that is distinct from free-living cells. This result suggested an intricate association between extracellular matrix expression and hyphae colonization. In accordance, deletion epsD, tasA, or both epsD and tasA genes of B. velezensis diminished colonization of the T. guizhouense hyphae. The insights from our study demonstrate that soil BFIs are more complex than we understood, potentially involving both competition and cooperation. These intricate biofilm-mediated BFI dynamics might contribute to the remarkable diversity observed within soil microbiota, providing a fresh perspective for further exploration of BFIs in the plant rhizosphere.

microbiology↗

bioRxiv2024

Spatial Transcriptomics-Aided Localization for Single-Cell Transcriptomics with STALocator

Single-cell RNA-sequencing (scRNA-seq) techniques can measure gene expression at the single-cell resolution but lack spatial information. The spatial transcriptomics (ST) techniques simultaneously provide gene expression data and spatial information. However, the data quality on the spatial resolution or gene coverage is still much lower than the single-cell transcriptomics data. To this end, we develop a Spatial Transcriptomics-Aided Locator for single-cell transcriptomics (STALocator) to localize single cells to corresponding ST data. Applications on simulated data showed that STALocator performed better than other localization methods from different angles. When applied to human brain scRNA-seq data and dorsolateral prefrontal cortex 10x Visium data, STALocator could robustly reconstruct the laminar organization of layer-associated cell types. Applications on scRNA-seq data and Spatial Transcriptomics data of human squamous cell carcinoma illustrated that STALocator could robustly reconstruct the relative spatial relationship between tumor-specific keratinocytes, microenvironment-associated cell populations, and immune cells. Moreover, STALocator could enhance gene expression patterns for Slide-seqV2 data and predict genome-wide gene expression data for FISH data, leading to the identification of more spatially variable genes and more biologically relevant GO terms compared to raw data.

bioinformatics↗

bioRxiv2024

Channel width modulates the permeability of DNA origami based nuclear pore mimics

Nucleoporins (nups) in the central channel of nuclear pore complexes (NPCs) form a selective barrier that suppresses the diffusion of most macromolecules while enabling rapid transport of nuclear transport receptors (NTRs) with bound cargos. The complex molecular interactions between nups and NTRs have been thought to underlie the gatekeeping function of the NPC. Recent studies have shown considerable variation in NPC diameter but how altering NPC diameter might impact the selective barrier properties remains unclear. Here, we build DNA nanopores with programmable diameters and nup arrangement to mimic NPCs of different diameters. We use hepatitis B virus (HBV) capsids as a model for large-size cargos. We find that Nup62 proteins form a dynamic cross-channel meshwork impermeable to HBV capsids when grafted on the interior of 60-nm wide nanopores but not in 79-nm pores, where Nup62 cluster locally. Furthermore, importin-{beta}1 substantially changes the dynamics of Nup62 assemblies and facilitates the passage of HBV capsids through NPC mimics containing Nup62 and Nup153. Our study shows the transport channel width is critical to the permeability of nup barriers and underscores the role of NTRs in dynamically remodeling nup assemblies and mediating the nuclear entry of viruses.

biophysics↗

bioRxiv2024

Curved light sheet microscopy for centimeter-scale cleared tissues imaging

Imaging large cleared tissues requires scaling the throughput of imaging techniques. Here we introduce curved light sheet microscope to perform optical sectioning with curved light sheets. This concept addresses the long-standing field curvature problem and lowers the barriers in designing high-throughput objectives. Leveraging a customized objective, the curved light sheet microscope achieves diffraction-limited resolution (1.0 m laterally and 2.5 m axially) and uniform contrast over a field of view of more than 1 x 1 cm2 and is compatible with various tissue clearing techniques. Imaging an entire intact cleared mouse brain at 0.625 x 0.625 x 1.25 m3 voxel size takes less than 3 hours and image tiling is not required. We share full optics description of the objective and report imaging neuronal and vascular networks and tracing brain-wide long-distance axonal projections in intact mouse brains.

bioengineering↗

bioRxiv2024

Optimization of an adeno-associated viral vector for keratinocytes in vitro and in vivo

BackgroundLocal gene therapies, including in vivo genome editing, are highly anticipated for the treatment of genetic diseases in skin, especially the epidermis. While the adeno-associated virus (AAV) is a potent vector for in vivo gene delivery, the lack of efficient gene delivery methods has limited its clinical applications. ObjectiveTo optimize the AAV gene delivery system with higher gene delivery efficiency and specificity for epidermis and keratinocytes (KCs), using AAV capsid and promoter engineering technologies. MethodsAAV variants with mutations in residues reported to be critical to determine the tropism of AAV2 for KCs were generated by site-directed mutagenesis of AAVDJ. The infection efficiency and specificity for KCs of these variants were compared with those of previously reported AAVs considered to be suitable for gene delivery to KCs in vitro and in vivo. Additionally, we generated an epidermis-specific promoter using the most recent short-core promoter and compared its specificity with existing promoters. ResultsA novel AAVDJ variant capsid termed AAVDJK2 was superior to the existing AAVs in terms of gene transduction efficiency and specificity for epidermis and KCs in vitro and in vivo. A novel tissue-specific promoter, termed the K14 SCP3 promoter, was superior to the existing promoters in terms of gene transduction efficiency and specificity for KCs. ConclusionThe combination of the AAVDJK2 capsid and K14 SCP3 promoter improves gene delivery to epidermis in vivo and KCs in vitro. The novel AAV system may benefit experimental research and development of new epidermis-targeted gene therapies.

bioengineering↗

bioRxiv2024

Mechanically Sheared Axially Swept Light-Sheet Microscopy

We present a mechanically sheared image acquisition format for upright and open-top light-sheet microscopes that automatically places data in its proper spatial context. This approach, which reduces computational post-processing and eliminates unnecessary interpolation or duplication of the data, is demonstrated on an upright variant of Axially Swept Light-Sheet Microscopy (ASLM) that achieves a field of view, measuring 774 x 435 microns, that is 3.2-fold larger than previous models and a raw and isotropic resolution of [~]420 nm. Combined, we demonstrate the power of this approach by imaging sub-diffraction beads, cleared biological tissues, and expanded specimens.

biophysics↗

bioRxiv2024

Molecular insights into the atypical activation mechanism of GPR156 in maintaining auditory function

The class C orphan GPCR GPR156, which lacks the typical extracellular region, plays a pivotal role in auditory function through Gi2/3. Here, we demonstrate that GPR156 with high constitutive activity is essential for maintaining auditory function, and we further present two cryo-EM structures of human GPR156. The GPR156 dimer in both the apo state and Gi3 protein-coupled state adopt a TM5/6-TM5/6 interface, indicating the high constitutive activity of GPR156 in the apo state. The C-terminus plays a dual role in promoting G protein binding within G-bound subunit while preventing the G-free subunit from binding to additional G protein. These observations explain how GPCR activity is maintained through dimerization and provide a mechanistic insight into the sustained role of GPR156 in maintaining auditory function.

molecular biology↗

bioRxiv2024

Microbial community assembly during aging of food waste-derived hydrochar: key bacterial guilds mediate nutrient dynamics

Hydrochar aging may mitigate the adverse effects of direct application on plant growth. However, little is known about the strategies for accelerating this process and the microbiological mechanisms involved. This study explored the effects of three strategies, including the additions of straw and efficient-degrading microorganisms, on the aging processes of food waste-derived hydrochar, and the key microbial drivers. The bacterial and fungal community compositions in hydrochar were estimated at different aging periods (i.e., day 1, 7, 14 and 35) using 16S and ITS rRNA gene sequencing. The results showed that straw and microbial inoculum addition improved the temperature and shortened the aging time by [~]30%. Three bacterial guilds, mainly including Bacillus-like species, were identified that had significant correlations with the nitrogen (N) and phosphorus (P) dynamics during aging. This study demonstrates the feasibility of manipulating key microbial guilds artificially to achieve efficient harmless-treatment of hydrochar. HighlightsO_LIStraw and microbial inoculum addition reduced ageing duration by 30%. C_LIO_LIMicrobial inoculum addition increases the aging reaction temperature by 13%. C_LIO_LIBacteria, rather than fungi, play the critical role in hydrochar aging. C_LIO_LIBacillus and related species drive nitrogen and phosphorus cycles of aging. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=155 SRC="FIGDIR/small/580608v1_ufig1.gif" ALT="Figure 1"> View larger version (68K): org.highwire.dtl.DTLVardef@b2c2c9org.highwire.dtl.DTLVardef@124ab1org.highwire.dtl.DTLVardef@e5c00borg.highwire.dtl.DTLVardef@1a31deb_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2024

navigate: an open-source platform for smart light-sheet microscopy.

navigate is a turnkey, open-source software solution designed to enhance light-sheet fluorescence microscopy (LSFM) by integrating smart microscopy techniques into a user-friendly framework. It enables automated, intelligent imaging with a Python-based control system that supports GUI-reconfigurable acquisition routines and the integration of diverse hardware sets. As a comprehensive package, navigate democratizes access to advanced LSFM capabilities, facilitating the development and implementation of smart microscopy workflows without requiring deep programming knowledge or specialized expertise in light-sheet microscopy.

biophysics↗

bioRxiv2024

Efficient 3D cone trajectory design for improved combined angiographic and perfusion imaging using arterial spin labeling

PurposeTo improve the spatial resolution and repeatability of a non-contrast MRI technique for simultaneous time resolved 3D angiography and perfusion imaging by developing an efficient 3D cone trajectory design. MethodsA novel parameterized 3D cone trajectory design incorporating the 3D Golden Angle was integrated into 4D combined angiography and perfusion using radial imaging and arterial spin labeling (CAPRIA) to achieve higher spatial resolution and sampling efficiency for both dynamic angiography and perfusion imaging with flexible spatiotemporal resolution. Numerical simulations and physical phantom scanning were used to optimize the cone design. Eight healthy volunteers were scanned to compare the original radial trajectory in 4D CAPRIA with our newly designed cone trajectory. A locally low rank reconstruction method was used to leverage the complementary k-space sampling across time. ResultsThe improved sampling in the periphery of k-space obtained with the optimized 3D cone trajectory resulted in improved spatial resolution compared with the radial trajectory in phantom scans. Improved vessel sharpness and perfusion visualization were also achieved in vivo. Less dephasing was observed in the angiograms due to the short echo time of our cone trajectory and the improved k-space sampling efficiency also resulted in higher repeatability compared to the original radial approach. ConclusionThe proposed 3D cone trajectory combined with 3D Golden Angle ordering resulted in improved spatial resolution and image quality for both angiography and perfusion imaging and could potentially benefit other applications that require an efficient sampling scheme with flexible spatial and temporal resolution.

neuroscience↗

bioRxiv2024

Self-balanced regulation by the long non-coding RNA Lockd on the cell cycle progression of cortical neural progenitor cells through counteracting cis and trans roles

Neural stem/progenitor cells (NSPCs) undergo active proliferation and exit the cell cycle upon precise regulation to produce differentiated progenies in order. Long non-coding RNAs (lncRNAs) have emerged as critical players in the developmental processes of NSPCs; however, relatively few have been shown to regulate the cell cycle in vivo directly. Here, we identified an NSPC-expressed lncRNA Lockd (lncRNA downstream of Cdkn1b) in the developing forebrain. Using in vivo loss of function models by premature termination of Lockd transcription via knockin polyadenylation signals or shRNA-mediated knockdown of Lockd (Lockd-KD), we show that Lockd is required for proper cell cycle progression of cortical NSPCs and the production of TBR2+ intermediate neural progenitor cells during cortical development. Interestingly, a comparison of genetic profiling in the two models reveals that Lockd promotes the expression of two counteracting cell cycle-related genes, Cdkn1b in cis and Ccnd1 in trans. Overexpression of Ccnd1 or Cdkn1b-KD can rescue the cellular phenotypes of reduced cycling progenitors in Lockd-KD. Our results imply that lncRNA could act through distinct cis and trans mechanisms to achieve a self-balanced function.

developmental biology↗

bioRxiv2024

A Novel Mouse Model for LAMA2-Related Muscular Dystrophy: Analysis of Molecular Pathogenesis and Clinical Phenotype

Our understanding of the molecular pathogenesis of LAMA2-related muscular dystrophy (LAMA2-MD) requires improving. Here, we report the phenotype, neuropathology and transcriptomics data (scRNA-seq and bulk RNA-seq) of a new Lama2 knockout mouse (dyH/dyH) which was created based on the human LAMA2-MD mutation hotspot region using CRISPR-Cas9. The dyH/dyH mice presented severe phenotype with muscular dystrophy. Mouse brain scRNA-seq showed that Lama2 gene was expressed predominantly and specifically in vascular and leptomeningeal fibroblasts and vascular smooth muscle cells, and weakly in astrocytes in wild-type mouse. Laminin 2 expression on the cortical surface was observed with immunofluorescence. In dyH/dyH, Lama2 expression was decreased in those cell types, which might be associated with the disruption of gliovascular basal lamina assembly. Additionally, transcriptomic investigation of muscles showed 2020 differentially expressed genes, mainly associated with the impaired muscle cytoskeleton and development. In summary, this study provided potentially useful information for understanding the molecular pathogenesis of LAMA2-MD.

neuroscience↗

bioRxiv2023

Cebranopadol, a novel long-acting opioid agonist with low abuse liability, to treat opioid use disorder: Preclinical evidence of efficacy

The gold standard pharmacological treatment for opioid use disorder (OUD) consists of maintenance therapy with long-acting opioid agonists such as buprenorphine and methadone. Despite these compounds having demonstrated substantial efficacy, a significant number of patients do not show optimal therapeutic responses. Moreover, the abuse liability of these medications remains a major concern. Cebranopadol, is a new, long-acting pan-opioid agonist that also activates the nociception/orphanin FQ NOP receptor. Here we used rats to explore the therapeutic potential of this agent in OUD. First, in operant intravenous self-administration experiments we compared the potential abuse liability of cebranopadol with the prototypical opioid heroin. Under a fixed ratio 1 (FR1) contingency, rats maintained responding for heroin (1, 7, 20, 60 g/inf) to a larger extent than cebranopadol (0.03, 0.1, 0.3, 1.0, 6.0 g/inf). When the contingency was switched to a progressive ratio (PR) reinforcement schedule, heroin maintained responding at high levels at all except the lowest dose. Conversely, in the cebranopadol groups responding decreased drastically and the break point (BP) did not differ from saline controls. Next, we demonstrated that oral administration of cebranopadol (0, 25, 50 g/kg) significantly attenuated drug self-administration independent of heroin dose (1, 7, 20, 60 g/inf). Cebranopadol also reduced the break point for heroin (20 g/inf). Furthermore, in a heroin self-administration training extinction/reinstatement paradigm, pretreatment with cebranopadol significantly attenuated yohimbine stress-induced reinstatement of drug seeking. Together, these data indicate that cebranopadol has limited abuse liability compared to heroin and is highly efficacious in attenuating opioid self-administration and stress-induced reinstatement, suggesting clinical potential of this compound for OUD treatment.

pharmacology and toxicology↗