Biology subjects

Qiu, G.

Publications and source records attributed to Qiu, G..

At least 19 recordsLinked to original sources

bioRxiv2026

Cortex-wide single-cell activity mapping in freely moving mice

How the cortex supports complex, naturalistic behavior can be revealed only in freely moving animals. Although head-mounted microscopes promise access to the neural dynamics underlying such behavior, fundamental trade-offs among field of view, spatial resolution, device weight, and background contamination have prevented cortex-wide single-neuron recording, leaving distributed cortical coordination largely inaccessible. To meet these challenges, we introduce COMET (Cortex-wide Observational Miniature Epifluorescence Technique), a 3.75-g head-mounted mesoscope that integrates an aberration-controlled wide-field optical design, uniform high-efficiency excitation and single-coaxial power-and-data transmission with an end-to-end denoising and signal-extraction pipeline. This enables cortex-wide calcium imaging at single-cell resolution in freely moving mice. COMET captures activity from >15,000 layer 2/3 neurons per 5-min recording over fields of view up to 10 mm in diameter while preserving natural behavior. Benchmarking against benchtop two-photon microscopy demonstrates high spatial concordance of detected neurons and matched event-level calcium dynamics. We apply COMET to social interaction to quantify region-specific engagement and to an auditory trace fear-conditioning task that requires natural movement and behavioral expression, revealing time-ordered changes in regional firing-rate structure and functional connectivity preceding a global conditioned response. COMET provides an open, lightweight hardware-software framework for linking single-neuron activity to cortex-scale network dynamics during freely expressed behaviors under changing internal or external conditions.

neuroscience↗

bioRxiv2026

A spatiotemporal immune atlas of subarachnoid hemorrhage from single-cell and spatial transcriptomics

Background and PurposeSubarachnoid hemorrhage (SAH) triggers a complex immune response that critically influences early brain injury (EBI) and long-term outcomes. However, the precise spatiotemporal dynamics and heterogeneity of immune cell infiltration and microglial reprogramming remain poorly understood. We aimed to construct a high-resolution immune atlas to delineate cell states, lineage trajectories, and spatial niches following SAH. MethodsWe integrated single-cell RNA sequencing (scRNA-seq) of CD45+ immune cells with spatial transcriptomics (ST) in a murine endovascular perforation SAH model. Immune landscapes were profiled at 24 hours (acute phase) and 72 hours (subacute phase) post-injury, compared with sham controls. Advanced bioinformatics integrated transcriptional signatures with spatial localization to map macrophage, neutrophil, and microglial dynamics. ResultsOur atlas reveals a coordinated immune transition from acute inflammation to reparative processing. We identified five macrophage, four neutrophil, and eight microglial subsets with distinct spatiotemporal patterns. Notably, we discovered a SAH-specific inflammatory microglial population (MG_03; Spp1+/Lpl+) that clusters at the rupture site during the acute phase. This subset is transcriptionally distinct from disease-associated microglia (DAM) in other neurodegenerative conditions. Trajectory analysis suggests MG_03 acts as a signaling hub for immune recruitment before transitioning toward proliferative and reparative states (MG_06-08) that disperse into the parenchyma by 72 hours. ConclusionsThis study provides the first comprehensive spatiotemporal immune atlas of SAH, highlighting the distinct role of the Spp1+ MG_03 subpopulation in early injury sensing. These findings offer a roadmap for identifying precise therapeutic windows and targeting specific immune subsets to mitigate EBI. Graphical AbstractExperimental workflow for single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) in a mouse SAH model induced by endovascular perforation. Brain tissue from the ipsilateral (injured) hemisphere was collected from sham and at 24 h and 72 h post-SAH. For scRNA-seq, CD45 immune cells were isolated prior to library preparation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=124 SRC="FIGDIR/small/703421v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@4a1bc9org.highwire.dtl.DTLVardef@16664c4org.highwire.dtl.DTLVardef@1619725org.highwire.dtl.DTLVardef@a0d34_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Construction of a novel 3D urinary bladder mucosa model and its application in toxicity assessment of arsenicals

The urinary bladder is a major target organ for environmental toxicants, including arsenic. The objects of this study were two-fold. First, we constructed a novel 3D urinary bladder mucosa model that incorporated an overlying epithelium and a supporting subepithelial layer, referred to as the 3D-UBMM. Primary human bladder urothelial and fibroblast cells were immortalized by introducing the human CDK4R24C and TERT genes. The subsequent construction of the 3D-UBMM involved incorporating the immortalized fibroblast cells into a collagen raft, while the immortalized urothelial cells were cultured at the air-liquid interface of the raft. This 3D-UBMM closely resembles the human urinary bladder epithelium in terms of morphology and marker protein expression, including uroplakin 1b, P63, and cytokeratin 5. Second, using the 3D-UBMM we investigated the cytotoxicity of sodium arsenite (iAsIII) and dimethylarsenic acid (DMAV). Exposure to iAsIII and DMAV resulted in increased urothelial cell necrosis and increased {gamma}-H2AX-positive cells along with a reduction of P63-positive cells, and each of these effects was induced in a dose-response manner. These findings affirm that this novel 3D-UBMM closely resembles the human urinary bladder epithelial layer, offering a practical in vitro model for the evaluation of the toxicity of arsenic and other bladder carcinogens and the role of cancer-related genes in bladder carcinogenicity. In addition, by identifying mechanisms of carcinogenesis this model will aid in hazard identification and risk assessment of potential bladder carcinogens.

pharmacology and toxicology↗

bioRxiv2025

Developing a Novel In Vitro Toxicity Assay for Predicting Inhalation Toxicity in Rats

The development of alternative in vitro methods for assessing acute inhalation toxicity is a critical step toward reducing animal testing and aligns with the principles of the 3Rs (replacement, reduction, and refinement). In this study, we developed and optimized a neutral red uptake (NRU) assay using human lung adenocarcinoma cells (A549) as a predictive model (A549-NRU) for acute inhalation toxicity. To improve assay efficiency and robustness, we introduced two key modifications: the incubation time was reduced to 15 minutes to enable rapid and high-throughput screening, and for chemicals reactive with polystyrene 6-well glass plates were used to prevent chemical-induced degradation and ensure assay consistency. LC50 values were determined for 49 chemicals and compared with reported LC50 values from 4-hour rat inhalation studies. A significant positive correlation was observed between A549-NRU-derived LC50 values and in vivo LC50 values for water-soluble compounds and chemicals containing aldehyde, ketone, alcohol, ether, and epoxide functional groups, suggesting that in vivo LC50 values may be predictable using the A549-NRU assay. Additionally, A549-NRU LC50 values showed significant negative correlations with molecular weight and octanol-water partition coefficients, indicating that chemicals with higher values tended to be less cytotoxic in vitro. Importantly, the A549-NRU assay demonstrated stronger correlation with in vivo LC50 values than the conventional NRU assay using mouse 3T3 fibroblast cells. These findings support the use of the A549-NRU assay to estimate starting doses for in vivo studies, and potentially as an in vitro alternative for predicting acute inhalation toxicity. Impact statementThe optimized A549-NRU assay demonstrates predictive potential for inhalation toxicity while reducing reliance on animal testing. This model serves as a human-relevant alternative for estimating starting doses for in vivo inhalation toxicity studies.

pharmacology and toxicology↗

bioRxiv2024

From gene to structure: Unraveling genomic dark matter in Ca. Accumulibacter

Candidatus Accumulibacter is a unique and pivotal genus of polyphosphate-accumulating organisms (PAOs) prevalent in wastewater treatment plants, and plays mainstay roles in the global phosphorus cycle. Whereas, the efforts toward a complete understanding of their genetic and metabolic characteristics are largely hindered by major limitations in existing sequence-based annotation methods, leaving more than half of their protein-encoding genes unannotated. To address the challenge, we developed a comprehensive approach integrating pangenome analysis, gene-based protein structure and function prediction, and metatranscriptomic analysis, extending beyond the constraints of sequence-centric methodologies. The application to Ca. Accumulibacter allowed the establishment of the pan-Ca. Accumulibacter proteome structure database, providing references for >200,000 proteins. Benchmarking on 28 Ca. Accumulibacter genomes showed major increases in the average annotation coverage from 51% to 83%. Genetic and metabolic characteristics that had eluded exploration via conventional methods were unraveled. For instance, the identification of a previously unknown phosphofructokinase gene suggests that all Ca. Accumulibacter encoded a complete Embden-Meyerhof-Parnas pathway. A previously defined homolog of phosphate-specific transport system accessory protein (PhoU) was actually an inorganic phosphate transport (Pit) accessory protein, regulating Pit instead of the high-affinity phosphate transport (Pst), a key to the emergence of the polyphosphate-accumulating trait of Ca. Accumulibacter. Additional lineage members were found encoding complete denitrification pathways. This study offers a readily usable and transferable tool for the establishment of high-coverage annotation reference databases for diverse cultured and uncultured bacteria, facilitating the exploration and understanding of genomic dark matter in the bacterial domain. SynopsisA integrated and advanced approach unraveling key genomic dark matter in Ca. Accumulibacter and readily applicable to diverse bacteria for customerized high-coverage annotation reference database establishment

genomics↗

bioRxiv2024

Intermittent theta burst stimulation (iTBS)-induced changes of resting-state brain entropy (BEN)

Intermittent theta burst stimulation (iTBS) is a novel protocol of repetitive transcranial magnetic stimulation (rTMS). While iTBS has shown better therapeutic effects for depression than conventional high-frequency rTMS (HF-rTMS), its underlying neuronal mechanism remains elusive. Brain entropy (BEN), a measure of irregularity of brain activity, has recently emerged as a novel marker of regional brain activity. Our previous studies have shown the sensitivity of BEN to depression and HF-rTMS, suggesting BEN as a sensitive tool for understanding the brain mechanism of iTBS. To assess this possibility, we calculated BEN using resting state fMRI data provided by an open dataset in OpenNeuro. Sixteen healthy participants underwent 600 pulses of iTBS applied over the left dorsolateral prefrontal cortex (L-DLPFC) at two intensities (90% and 120% of individual resting motor threshold (rMT)) on separate days. We assessed the pre-post stimulation BEN difference and its associations with neurotransmitter receptor and transporter binding maps. Our results showed that subthreshold iTBS (90% rMT) decreased striatal BEN, while suprathreshold iTBS (120% rMT) increased striatal BEN. We also found significant differences in the spatial correlation between BEN changes induced by different stimulation intensities and various neurotransmitters. These results suggest that differences in BEN caused by iTBS stimulation intensity may be related to the release of other neurotransmitters. The study underscores the significance of iTBS stimulation intensity and provides a basis for future clinical investigations to identify stimulation intensities with good therapeutic benefits.

neuroscience↗

bioRxiv2024

Impaired central pattern generators due to abnormal EPHA4 signaling leads to idiopathic scoliosis

Idiopathic scoliosis (IS) is the most common form of spinal deformity with unclear pathogenesis. In this study, we firstly reanalyzed the loci associated with IS, drawing upon previous studies. Subsequently, we mapped these loci to candidate genes using either location-based or function-based strategies. To further substantiate our findings, we verified the enrichment of variants within these candidate genes across several large IS cohorts encompassing Chinese, East Asian, and European populations. Consequently, we identified variants in the EPHA4 gene as compelling candidates for IS. To confirm their pathogenicity, we generated zebrafish mutants of epha4a. Remarkably, the zebrafish epha4a mutants exhibited pronounced scoliosis during later stages of development, effectively recapitulating the IS phenotype. We observed that the epha4a mutants displayed defects in left-right coordination during locomotion, which arose from disorganized neural activation in these mutants. Our subsequent experiments indicated that the disruption of the central pattern generator (CPG) network, characterized by abnormal axon guidance of spinal cord interneurons, contributed to the disorganization observed in the mutants. Moreover, when knocked down efnb3b, the ligand for Epha4a, we observed similar CPG defects and disrupted left-right locomotion. These findings strongly suggested that ephrin B3-Epha4 signaling is vital for the proper functioning of CPGs, and defects in this pathway could lead to scoliosis in zebrafish. Furthermore, we identified two cases of IS in NGEF, a downstream molecule in the EPHA4 pathway. Collectively, our data provide compelling evidence that neural patterning impairments and disruptions in CPGs may underlie the pathogenesis of IS.

genetics↗

bioRxiv2024

A Novel Support Vector Machine-Based One-Day, Single-Dose Prediction Model of Genotoxic Hepatocarcinogenicity in Rats

The development of a rapid and accurate model for determining the genotoxicity and carcinogenicity of chemicals is crucial for effective cancer risk assessment, and it also contributes to cancer prevention. This study aims to develop a one-day, single-dose model for identifying genotoxic hepatocarcinogens (GHCs) in rats. Microarray gene expression data from the livers of rats administered a single dose of 58 compounds, including 5 GHCs, was obtained from the Open TG-GATEs database and used for the identification of marker genes and the construction of a predictive classifier to identify GHCs in rats. We identified 10 gene markers commonly responsive to all 5 GHCs and used them to construct a support vector machine-based predictive classifier. This classifier effectively distinguishes GHCs from other compounds, demonstrating 100% sensitivity and over 96% specificity. To further assess the models effectiveness and reliability, we conducted multi-institutional one-day single oral administration studies on rats. These studies examined 64 compounds, including 23 GHCs, with gene expression data of the marker genes obtained via quantitative PCR (qPCR) 24 hours after a single oral administration. Our results demonstrate that qPCR analysis is an effective alternative to microarray analysis. The GHC predictive model showed high accuracy and reliability, achieving a sensitivity of 91% (21/23) and a specificity of 93% (38/41) across multiple validation studies in three institutions. In conclusion, the present one-day single oral administration model proves to be a reliable and highly sensitive tool for identifying GHCs and is anticipated to be a valuable tool in identifying and screening potential GHCs.

pharmacology and toxicology↗

bioRxiv2022

Quantitatively mapping local quality of super-resolution microscopy by rolling Fourier ring correlation

In fluorescence microscopy, computational algorithms have been developed to suppress noise, enhance contrast, and even enable super-resolution (SR). However, the local quality of the images may vary on multiple scales, and these differences can lead to misconceptions, which is especially intractable in emerging deep-learning ones. Current mapping methods fail to finely estimate the local quality, challenging to associate the SR scale content. Here, we develop a rolling Fourier ring correlation (rFRC) framework to evaluate the reconstruction uncertainties down to SR scale. To visually pinpoint regions with low reliability, a filtered rFRC is combined with a modified resolution scaled error map (RSM), offering a comprehensive and concise map for further examination. We demonstrate their performances on various SR imaging modalities, and the resulting quantitative maps enable better SR images integrated from different reconstructions. Beyond that, we provide a strategy for learning-based restorations, allowing a direct detection of both data and model uncertainties, and expect the representative cases can inspire further advances in this rapidly developing field.

biophysics↗

bioRxiv2022

CRISPR-Cas phage defense systems and prophages in Candidatus Accumulibacter

Candidatus Accumulibacter is a key genus of polyphosphate-accumulating organisms (PAOs) found in laboratory- and full-scale wastewater treatment systems, mediating enhanced biological phosphorus removal (EBPR). However, little is known about their ability to resist phage infection. We conducted a systematic analysis of the occurrence and characteristics of clustered regularly interspaced short palindromic repeats and associated proteins (CRISPR-Cas) systems and prophages in diverse Ca. Accumulibacter taxa (43 in total, including 10 newly recovered genomes). Fourty complete CRISPR loci were identified in 28 genomes, falling into 6 subtypes. The occurrence and distribution of CRISPR-Cas systems did not follow a vertical evolutionary relationship. Phylogenetic analyses of the cas genes and direct repeats (DRs) suggested that the CRISPR-Cas systems were likely acquired via horizontal gene transfer, with acquisition rates higher than those of speciation, rendering different Ca. Accumulibacter distinct adaptivity to phage predations. 2448 spacers were identified, 67 of them matched to known phages. Major differences were observed among the numbers of spacers for different Ca. Accumulibacter, showing unique phages that could be resisted by different members. A comparison of the spacers in genomes having the same cas gene but from distinct geographical locations indicated that habitat isolation may have resulted in the acquisition of different spacers by different Ca. Accumulibacter. Metagenomic analysis allowed the identification of 26 viral contigs (18 are Caudovirales members) in 6 metagenomic datasets from three lab-scale enrichment reactors, matching to 73 spacers in 10 Ca. Accumulibacter genomes in these reactors, showing the specific immunity of these Ca. Accumulibacter. Metatranscriptomic analyses showed the activity of the CRISPR-Cas system under both anaerobic and aerobic conditions. Extra efforts were made to identify prophages in Ca. Accumulibacter genomes. In total, 133 prophage regions were identified. Twenty-seven of them were classified as potentially active prophages. Three prophages (all are Caudovirales members, in DS2011, SCELSE-7IIH and SCELSE-5IIH, respectively) are readily activable. Differences in the occurrence of CRISPR-Cas systems and prophages in Ca. Accumulibacter will lead to their distinct responses under phage predation. This study represents the first systematic analysis of CRISPR-Cas systems and prophages with combined experimental and bioinformatic methods in the Ca. Accumulibacter lineage, providing new perspectives on the potential impacts of phages on Ca. Accumulibacter and EBPR systems.

bioinformatics↗

bioRxiv2022

Zinc Fingers and Homeoboxes 2 is Required for Diethylnitrosamine-induced Liver Tumor Formation in C57BL/6 Mice

Liver cancer, comprised mainly of hepatocellular carcinoma (HCC), is the third leading cause of cancer deaths worldwide and increasing in Western countries. We previously identified the transcription factor Zinc Fingers and Homeoboxes 2 (Zhx2) as a regulator of hepatic gene expression, and many Zhx2 target genes are dysregulated in HCC. Here, we investigate HCC in Zhx2-deficient mice using the Diethylnitrosamine (DEN)-induced liver tumor model. Our study using whole-body Zhx2 knock-out (Zhx2KO) mice revealed the complete absence of liver tumors 9 and 10 months after DEN exposure.Analysis soon after DEN treatment showed no differences in expression of the DEN bioactivating enzyme CYP2E1 and DNA polymerase delta 2, or in the numbers of {gamma}H2AX foci between Zhx2KO and wild-type (Zhx2wt) mice. The absence of Zhx2, therefore, did not alter DEN bioactivation or DNA damage. Zhx2KO livers showed fewer positive foci for Ki67 staining and reduced IL-6 and AKT2 expression compared to Zhx2wt livers, suggesting that Zhx2 loss reduces liver cell proliferation and may account for reduced tumor formation. Tumors were reduced but not absent in DEN-treated liver-specific Zhx2 knock-out mice, suggesting that Zhx2 acts in both hepatocytes and non-parenchymal cells to inhibit tumor formation. Analysis of data from The Cancer Genome Atlas and Clinical Proteomic Tumor Consortium indicated that ZHX2 mRNA and protein levels were significantly higher in HCC patients and associated with clinical pathological parameters. ConclusionsIn contrast to previous studies in human hepatoma cell lines and other HCC mouse models showing that Zhx2 acts as a tumor suppressor, our data indicate that Zhx2 acts as an oncogene in the DEN-induced HCC model and is consistent with the higher ZHX2 expression in HCC patients.

cancer biology↗

bioRxiv2022

Response of the plant core microbiome to Fusarium oxysporum infection and identification of the pathobiome.

Plant core microbiomes consist of persistent key members that provide critical host functions, but their assemblages can be interrupted by biotic and abiotic stresses. The pathobiome is comprised of dynamic microbial interactions in response to disease status of the host. Hence, identifying variation in the core microbiome and pathobiome can significantly advance our understanding of microbial-microbial interactions and consequences for disease progression and host functions. In this study, we combined glasshouse and field studies to analyse the soil and plant rhizosphere microbiome of cotton plants (Gossypium hirsutum) in the presence of a cotton-specific fungal pathogen, Fusarium oxysporum f. sp. vasinfectum (FOV). We found that FOV directly and consistently altered the rhizosphere microbiome, but the biocontrol agents enabled microbial assemblages to resist pathogenic stress. Using co-occurrence network analysis of the core microbiome, we identified the pathobiome comprised of the pathogen and key associate phylotypes in the cotton microbiome. Isolation and application of some negatively correlated pathobiome members provided protection against plant infection. Importantly, our field survey from multiple cotton fields validated the pattern and responses of core microbiomes under FOV infection. This study advances key understanding of core microbiome responses and existence of plant pathobiomes, which provides a novel framework to better manage plant diseases in agriculture and natural settings.

microbiology↗

bioRxiv2022

The dynamics of protein localisation to restricted zones within Drosophila mechanosensory cilia

The Drosophila chordotonal neuron cilium is the site of mechanosensory transduction. The cilium has a 9+0 axoneme structure and is highly sub-compartmentalised, with proximal and distal zones harbouring different TRP channels and the proximal zone axoneme also being decorated with axonemal dynein motor complexes. The activity of the dynein complexes is essential for mechanotransduction. We investigate the localisation of TRP channels and dynein motor complexes during ciliogenesis. Differences in timing of TRP channel localisation correlate with order of construction of the two ciliary zones. Dynein motor complexes are initially not confined to their target proximal zone, but complexes beyond the proximal zone are later cleared, perhaps by retrograde transport. Differences in transient distal localisation of ODAs and IDAs are consistent with previous suggestions from unicellular eukaryotes of differences in processivity during intraflagellar transport. Stable localisation depends on the targeting of their docking proteins in the proximal zone. For outer dynein arm (ODA) complexes, we characterise an ODA docking complex (ODA-DC) that is targeted directly to the proximal zone. Interestingly, the subunit composition of the ODA-DC in chordotonal neuron cilia appears to be different from the predicted ODA-DC in Drosophila sperm.

cell biology↗

bioRxiv2021

Mining endophytic microbiome information from plant and animal transcriptome data

Endophytic microorganisms play important physiological functions in plants and animals. In this paper, we developed a method to obtain endophytic microbiome information directly by analyzing transcriptome sequencing data files of plants and animals. Compared with the use of amplicon analysis or whole-genome sequencing of animal and plant tissues to analyze microbial composition information, this method can obtain endophytic microbiome information in addition to obtaining gene expression information of host plants and animals.

bioinformatics↗

bioRxiv2021

Global warming readiness: Feasibility of enhanced biological phosphorus removal from wastewater at 35oC

Recent research has shown enhanced biological phosphorus removal (EBPR) from municipal wastewater at warmer temperatures around 30{degrees}C to be stable in both laboratory-scale reactors and full-scale treatment plants. In the context of a changing climate, the feasibility of EBPR at even higher temperatures is of interest. We operated two lab-scale EBPR sequencing batch reactors with alternating anaerobic and aerobic phases for over 300 days at 30{degrees}C and 35{degrees}C, respectively, and followed the dynamics of the communities of phosphorus accumulating organisms (PAOs) and competing glycogen accumulating organisms (GAOs) using a combination of 16S rRNA gene metabarcoding, quantitative PCR and fluorescent in-situ hybridization analyses. Stable and nearly complete P removal was achieved at 30{degrees}C; similarly, long term P removal was stable at 35{degrees}C with effluent PO43--P concentrations < 0.5 mg/L on half of all monitored days. Diverse and abundant Ca. Accumulibacter amplicon sequence variants were closely related to those found in temperate environments, suggesting that EBPR at this temperature does not require a highly specialized PAO community. The slow-feeding strategy used effectively limited the carbon uptake rates of GAOs, allowing PAOs to outcompete GAOs at both temperatures. Candidatus Competibacter was the main GAO, along with cluster III Defluviicoccus members. These organisms withstood the slow-feeding regime, suggesting that their bioenergetic characteristics of carbon uptake differ from those of their tetrad-forming relatives. This specific lineage of GAOs warrants further study to establish how complete P removal can be maintained. Comparative cycle studies at two temperatures for each reactor revealed higher activity of Ca. Accumulibacter when the temperature was increased from 30{degrees}C to 35{degrees}C, suggesting that the stress was a result of the higher carbon (and/or P) metabolic rates of PAOs and GAOs, the resultant carbon deficiency, and additional community competition. An increase in the TOC to PO43--P ratio (from 25:1 to 40:1) effectively eased the carbon deficiency and benefited the proliferation of PAOs. In general, the slow-feeding strategy and sufficiently high carbon input benefited a high and stable EBPR at elevated temperature and represent basic conditions for full-scale applications.

microbiology↗

bioRxiv2020

Analysis procedures for assessing recovery of high quality, complete, closed genomes from Nanopore long read metagenome sequencing

New long read sequencing technologies offer huge potential for effective recovery of complete, closed genomes from complex microbial communities. Using long read (MinION) obtained from an ensemble of activated sludge enrichment bioreactors, we 1) describe new methods for validating long read assembled genomes using their counterpart short read metagenome assembled genomes; 2) assess the influence of different correction procedures on genome quality and predicted gene quality and 3) contribute 21 new closed or complete genomes of community members, including several species known to play key functional roles in wastewater bioprocesses: specifically microbes known to exhibit the polyphosphate- and glycogen-accumulating organism phenotypes (namely Accumulibacter and Dechloromonas, and Micropruina and Defluviicoccus, respectively), and filamentous bacteria (Thiothrix) associated with the formation and stability of activated sludge flocs. Our findings further establish the feasibility of long read metagenome-assembled genome recovery, and demonstrate the utility of parallel sampling of moderately complex enrichments communities for recovery of genomes of key functional species relevant for the study of complex wastewater treatment bioprocesses.

bioinformatics↗

bioRxiv2020

P4HA2, a prognostic factor, promotes glioma proliferation, invasion, migration and EMT through collagen regulation and PI3K/AKT pathway

Prolyl-4-hydroxylase subunit 2 (P4HA2), as a member of collagen modification enzymes, is induced under hypoxic conditions with essential roles in the collagen maturation, deposition as well as the remodeling of extracellular matrix(ECM). Mounting evidence has suggested that deregulation of P4HA2 is common in cancer. However, the expression pattern and molecular mechanisms of P4HA2 in glioma remain unknown. Here, we demonstrate that P4HA2 is overexpressed in glioma and inversely correlates with patient survival. Knockdown of P4HA2 inhibits proliferation, migration, invasion, and epithelial-to-mesenchymal transition (EMT)-like phenotype of glioma cells in vitro and suppressed tumor xenograft growth in vivo. Mechanistically, bioinformatics analysis shows that ECM-receptor interaction and PI3K/AKT pathway are the most enriched pathways of the co-expressed genes with P4HA2. Furthermore, P4HA2 mRNA was positively correlated with mRNA expressions of a series of collagen genes, but not mRNA of PI3K or AKT1/2. Conversely, both the protein expressions of collagens and phosphorylated PI3K/AKT could be downregulated either by silencing of P4HA2 expression or inhibition of its prolyl hydroxylase. Moreover, the inhibitory effects on the migration, invasion and the EMT-related molecules by P4HA2 knockdown can be recapitulated by the Akt phosphorylation activator. Taken together, our findings for the first time reveal an oncogenic role of P4HA2 in the glioma malignancy. By regulating the expression of fibrillar collagens and the downstream PI3K/AKT signaling pathway, it may serve as a potential anti-cancer target for the treatment of glioma. HighlightsP4HA2 is overexpressed and correlated with poor prognosis in glioma. P4HA2 depletion inhibits glioma proliferation, migration, invasion and EMT-like phenotype in vitro and tumorigenesis in vivo. P4HA2 depletion attenuates the PI3K/AKT signaling pathway in a collagen-dependent manner.

cancer biology↗

bioRxiv2019

Genetic and molecular mechanism for distinct clinical phenotypes conveyed by allelic truncating mutations implicated in FBN1

The molecular and genetic mechanisms by which different single nucleotide variant (SNV) alleles in specific genes, or at the same genetic locus, bring about distinct disease phenotypes often remain unclear. Allelic truncating mutations of fibrillin-1(FBN1) cause either classical Marfan syndrome (MFS) or a more severe phenotype associated with Marfanoid-progeroid-lipodystrophy syndrome (MPLS). A total of three Marfan syndrome/Marfanoid patients (2 singletons and 1 parent-offspring trio) were recruited. Targeted next-generation sequencing was performed on all the participants. We analyzed the molecular diagnosis, patient clinical features, and the potential molecular mechanism involved in the MPLS subject in our cohort. We investigated a small cohort, consisting of two classical MFS and one MPLS patient from China, whose clinical presentation included scoliosis potentially requiring surgical intervention. We provide evidence that most nonsense and frameshift mutations lead to FBN1 null alleles due to mutant mRNA transcript degradation. In contrast, the more severe disease phenotype, MPLS, is caused by mutant mRNAs that are predicted to escape the nonsense mediated decay (NMD) surveillance pathway, making a mutant protein that exerts a dominant negative interference effect to FBN1 thus generating a gain-of-function (GoF) rather than a loss-of-function (LoF) allele as in MFS. Overall, we provide direct evidence that a dominant negative interaction of FBN1 potentially explains the distinct clinical phenotype in MPLS patients through genetic and functional analysis of the first Chinese patient with MPLS. Moreover, our study expands the mutation spectrum of FBN1 and highlights the potential molecular mechanism for MPLS patients.

genetics↗