Biology subjects

Fang, L.

Publications and source records attributed to Fang, L..

At least 109 records · Page 6Linked to original sources

bioRxiv2020

In vitro culture of aberrant basal-like cells from fibrotic lung tissue

RationaleIn idiopathic pulmonary fibrosis (IPF) atypical epithelial cells are present in the alveolar compartment. Their origin and contribution to IPF pathogenesis is unknown. We recently cultured a distinct population of cells, which readily grew from fibrotic lung tissue, but only rarely from non-fibrotic tissue. Here we aimed to characterize these fibrosis-enriched cells and determine transcriptomic differences between cells derived from IPF and patients with other interstitial lung diseases (ILD). MethodsCells were cultured from peripheral lung tissue of ILD patients and analysed by bulk or single cell RNA sequencing (scRNA-seq), TaqMan-PCR, immunofluorescence (IF), immunoblotting or electron microscopy (EM). ResultsscRNA-seq demonstrated an overall homogeneity and epithelial origin of the cells. The majority of cells expressed basal cell markers (Cytokeratin (KRT) 5 and 17, TP63), of which a fraction co-expressed mesenchymal cell markers (VIM, FN1, CDH2), alveolar (SLC34A2, ABCA3, LPCAT1, EMP2, HOPX) and/or secretory epithelial cell markers (SCGB1A1, MUC4). Interestingly, most of the cells showed closest transcriptomic similarity to recently described aberrant basal-like cells. Cells derived from IPF versus other ILD patients revealed significant transcriptomic differences with an up-regulation of fibrosis-associated and a down-regulation of inflammatory pathways in IPF cells. ConclusionWe here confirm the presence of aberrant basal-like cells in fibrotic lung tissue and, importantly, are the first to describe their in vitro characteristics and a way of culturing these cells in vitro. Cultured basal-like cells co-express epithelial and mesenchymal markers, suggesting a partial epithelial to mesenchymal transition (EMT). A subset of cells co-express alveolar, ciliated or secretory epithelial cell markers, possibly indicating differentiation towards these cell linages. Furthermore, cultured basal-like cells display a disease-specific transcriptome, possibly induced by their specific microenvironment. Our findings will contribute to a better understanding of the cells origin and their potential contribution to IPF pathogenesis.

cell biology↗

bioRxiv2020

Combination of ipratropium bromide and salbutamol in children and adolescents with asthma: a meta-analysis

BackgroundA combination of ipratropium bromide (IB) and salbutamol is commonly used to treat asthma in children and adolescents; however, there has been a lack of consistency in its usage in clinical practice. ObjectiveTo evaluate the efficacy and safety of IB + salbutamol in the treatment of asthma in children and adolescents. MethodsThe MEDLINE, Embase, and Cochrane Library as well as other Chinese biomedical databases (including China Biological Medicine Database, Chinese National Knowledge Infrastructure, Chongqing VIP, and Wanfang Chinese language bibliographic database) were systematically searched from the date of database inception to 02/09/2019 for randomized controlled trials in children and adolescents ([≤]18 years) with asthma who received IB + salbutamol or salbutamol alone. The primary outcomes included hospital admission and adverse events. A random effects model with a 95% confidence interval (CI) was used. Subgroup analysis was performed according to age, severity of asthma, and co-interventions with other asthma controllers. This study was registered with PROSPERO. ResultsOf the 637 studies that were identified, 55 met the inclusion criteria and involved 6396 participants. IB + salbutamol significantly reduced the risk of hospital admission compared with salbutamol alone (risk ratio [RR] 0.79; 95% CI 0.66-0.95; p = 0.01; I2 = 40%). Subgroup analysis only showed significant difference in the risk of hospital admission in participants with severe asthma exacerbation (RR 0.71; 95% CI 0.60-0.85; p = 0.0001; I2 = 0%) and moderate-to-severe exacerbation (RR 0.69; 95% CI 0.50-0.96; p = 0.03; I2 = 3%). There were no significant differences in the risk of adverse events between IB + salbutamol group and salbutamol alone group (RR 1.77; 95% CI 0.63-4.98). ConclusionIB + salbutamol may be more effective than salbutamol alone for the treatment of asthma in children and adolescents, especially in those with severe and moderate to severe asthma exacerbation. Future prospective research on these subgroup population are needed.

pharmacology and toxicology↗

bioRxiv2020

FGFR Signaling Coordinates the Balance Between Glycolysis and Fatty Acid β-Oxidation in Lymphatic Endothelial Cells

The balance between glycolysis and oxidative phosphorylation is believed to be critical for maintaining cellular bioenergetics, yet the regulation of such balance in lymphatic endothelial cells (LECs) remains unclear. Here we found that chemical inhibition of fibroblast growth factor receptor (FGFR) activity or knockdown of FGFR1, which has been shown to suppress glycolysis and consequently ATP production, induces substantial upregulation of fatty acid {beta}-oxidation (FAO), but not glucose oxidation or glutamine oxidation in LECs. Mechanistically, blockade of FGFR-AKT signaling promotes the expression of CPT1A, a rate-limiting enzyme of FAO, in a PPAR-dependent manner. Metabolic analysis further showed that CPT1A depletion impairs ATP generation in FGFR1-deficient rather than wild-type LECs. This result suggests that FAO, which makes a minor contribution to cellular energy under normal conditions, can compensate for energy deficiency caused by FGFR inhibition. Consequently, CPT1A silencing potentiates the effect of FGFR1 knockdown on impeding LEC proliferation and migration. Collectively, our study identified an FGFR-regulated metabolic balance that is important for LEC growth.

cell biology↗

bioRxiv2020

Immunoglobulin fragment F(ab')2 against RBD potently neutralizes SARS-CoV-2 in vitro

COVID-19 caused by the emerging human coronavirus, SARS-CoV-2, has become a global pandemic, leading a serious threat to human health. So far, there is none vaccines or specific antiviral drugs approved for that. Therapeutic antibodies for SARS-CoV-2, was obtained from hyper immune equine plasma in this study. Herein, SARS-CoV-2 RBD with gram level were obtained through Chinese hamster ovary cells high-density fermentation. The binding of RBD to SARS-CoV-2 receptor, human ACE2, was verified and the efficacy of RBD in vivo was tested on mice and then on horses. As a result, RBD triggered high-titer neutralizing antibodies in vivo, and immunoglobulin fragment F(ab)2 was prepared from horse antisera through removing Fc. Neutralization test demonstrated that RBD-specific F(ab)2 inhibited SARS-CoV-2 with EC50 at 0.07 g/ml, showing a potent inhibitory effect on SARS-CoV-2. These results highlights as RBD-specific F(ab)2 as therapeutic candidate for SARS-CoV-2.

pharmacology and toxicology↗

bioRxiv2020

Potential Functions of Histone H3.3K56 Acetylation in Mammals

H3K56 acetylation (H3K56Ac) was first identified in yeast and has recently been reported to play important roles in maintaining genomic stability, chromatin assembly, DNA replication, cell cycle progression and DNA repair. Although H3.1K56Ac has been relatively well studied, the function of H3.3K56Ac remains mostly unknown in mammals. In this study, we used H3.3K56Q and H3.3K56R mutants to study the possible function of H3.3K56 acetylation. The K-to-Q substitution mimics a constitutively acetylated lysine, while the K-to-R replacement mimics a constitutively unmodified lysine. We report that cell lines harboring mutation of H3.3K56R exhibit dramatic morphology changes and cell death. Using Tet-Off inducible system, we show an increased population of polyploid/aneuploid cells and a decreased cell viability in H3.3K56R mutant cells. In consistence with these results, H3.3K56R mutant compromised H3.3 incorporation into several pericentric and centric heterochromatin regions we tested. Moreover, mass spectrometry analysis coupled with label free quantification reveal that biological processes regulated by the H3.3-associating proteins, whose interaction with H3.3 is markedly increased by H3.3K56Q mutation but decreased by H3.3K56Q mutation, include sister chromatid cohesion, mitotic nuclear division, and mitotic nuclear envelope disassembly. These results suggest that H3.3K56 acetylation is crucial for chromosome segregation and cell division in mammals.

molecular biology↗

bioRxiv2020

Implications of error-prone long-read whole-genome shotgun sequencing on characterizing reference microbiomes

Long-read sequencing techniques, such as the Oxford Nanopore Technology, can generate reads that are tens of kilobases in length, and are therefore particularly relevant for microbiome studies. However, due to the higher per-base error rates than typical short-read sequencing, the application of long-read sequencing on microbiomes remains largely unexplored. Here we deeply sequenced two human microbiota mock community samples (HM-276D and HM-277D) from the Human Microbiome Project. We showed that assembly programs consistently achieved high accuracy (~99%) and completeness (~99%) for bacterial strains with adequate coverage. We also found that long-read sequencing provides accurate estimates of species-level abundance (R=0.94 for 20 bacteria with abundance ranging from 0.005% to 64%). Our results demonstrate the feasibility to characterize complete microbial genomes and populations from error-prone Nanopore sequencing data, but also highlight necessary bioinformatics improvements for future metagenomics tool development.

genomics↗

bioRxiv2020

Genome-wide targets identification by CRISPRi-Omics for high-titer production of free fatty acids in Escherichia coli

To construct a superior microbial cell factory for chemical synthesis, a major challenge is to fully exploit cell potential via identifying and engineering beneficial gene targets in the sophisticated metabolic networks. Here, we develop an approach that integrates CRISPR interference (CRISPRi) to readily modulate genes expression and omics analyses to identify potential targets in multiple cellular processes, enabling systematical discovery of beneficial chromosomal gene targets that can be engineered to optimize free fatty acids (FFAs) production in Escherichia coli. We identify 56 beneficial genes via synergistic CRISPRi-Omics strategy, including 46 novel targets functioning in cell structure and division, and signaling transduction that efficiently facilitate FFAs production. Upon repressing ihfA and overexpressing aidB and tesA in E. coli, the recombinant strain LihfA-OaidB results in a FFAs titer of 21.6 g L-1 in fed-batch fermentation, which, to our best knowledge, is the maximum FFAs titer by the recombinant E. coli reported to date.

biochemistry↗

bioRxiv2020

Role of RgsA in oxidative stress resistance in Pseudomonas aeruginosa

Pseudomonas aeruginosa is an extremely common opportunistic pathogen in clinical practice. Patients with metabolic disorders, hematologic diseases, malignancies, who have undergone surgery or who have received certain treatments are susceptible to this bacterium. In addition, P. aeruginosa is a multidrug-resistant that tends to form biofilms and is refractory to treatment. Small regulatory RNAs are RNA molecules that are 40-500 nucleotides long, possess regulatory function, are ubiquitous in bacteria, and are also known as small RNA (sRNA). sRNAs play important regulatory roles in various vital life processes in diverse bacteria and their quantity and diversity of regulatory functions exceeds that of proteins. In this study, we showed that deletion of the sRNA RgsA decreases the growth rate and ability to resist different concentrations and durations of peroxide in P. aeruginosa. These decreases occur not only in the planktonic state, but also in the biofilm state. Finally, protein mass spectrometry was employed to understand changes in the entire protein spectrum. The results presented herein provide a description of the role of RgsA in the life activities of P. aeruginosa at the molecular, phenotypic, and protein levels.

microbiology↗

bioRxiv2019

Tuft cells restrain pancreatic tumorigenesis through paracrine eicosanoid signaling

Despite numerous advances in our understanding of pancreatic ductal adenocarcinoma (PDA) genetics and biology, this disease is expected to become the second leading cause of cancer-related U.S. deaths within the next few years. Incomplete understanding of how it arises precludes development of early detection and interception strategies to improve therapeutic outcomes. Acinar to ductal metaplasia involving genesis of tuft cells is one early step in PDA formation, but their functional significance has remained obscure due to their rarity and a lack of methods and relevant animal models for their molecular and functional analysis. Here, we show that deletion of tuft cell master regulator Pou2f3 eliminates pancreatic tuft cells and increases fibrosis, alters immune cell activation, and accelerates disease progression. We demonstrate that tuft cell expression of the prostaglandin D2 synthase Hpgds restrains pancreatic disease progression in early stages by inhibiting stromal activation. Analyses of human data sets are consistent with mouse studies. We propose that tuft cells and, by inference, the associated metaplastic lesions, play a protective role early in pancreatic tumorigenesis. SignificanceWe find that tuft cell formation in response to oncogenic Kras is protective and restrains tumorigenesis through local production of anti-inflammatory substances, including paracrine prostaglandin D2 signaling to the stroma. Our findings establish tuft cells as a metaplasia-induced tumor suppressive cell type.

cancer biology↗

bioRxiv2019

Polycomb-mediated repression compensates for loss of postnatal DNA methylation in excitatory neurons

Two epigenetic pathways of repression, DNA methylation and Polycomb repressive complex 2 (PRC2) mediated gene silencing, regulate neuron development and function, but their respective contributions are unknown. We found that conditional loss of the de novo DNA methyltransferase Dnmt3a in mouse excitatory neurons altered expression of synapse-related genes, stunted synapse maturation, and impaired working memory and social interest. Loss of Dnmt3a abolished postnatal accumulation of CG and non-CG DNA methylation, leaving neurons with an unmethylated, fetal-like epigenomic pattern at -140,000 genomic regions. The PRC2-associated histone modification H3K27me3 increased at many of these sites, partially compensating for the loss of DNA methylation. Our data support a dynamic interaction between two fundamental modes of epigenetic repression during postnatal maturation of excitatory neurons, which together confer robustness on neuronal regulation.

neuroscience↗

bioRxiv2019

eVIP2: Expression-based variant impact phenotyping to predict the function of gene variants

While advancements in genome sequencing have identified millions of somatic mutations in cancer, their functional impact is poorly understood. We previously developed the expression-based variant impact phenotyping (eVIP) method to use gene expression data to characterize the function of gene variants. The eVIP method uses a decision tree-based algorithm to predict the functional impact of somatic variants by comparing gene expression signatures induced by introduction of wild-type versus mutant cDNAs in cell lines. The method distinguishes between variants that are gain-of-function, loss-of-function, change-of-function, or neutral. We present eVIP2, software that allows for pathway analysis (eVIP Pathways) and usage with RNA-seq data. To demonstrate the eVIP2 software and approach, we characterized two recurrent frameshift variants in RNF43, a negative regulator of Wnt signaling, frequently mutated in colorectal, gastric and endometrial cancer. RNF43 WT, RNF43 R117fs, RNF43 G659fs, or GFP control cDNA were overexpressed in HEK293T cells. Analysis with eVIP2 predicted that the frameshift at position 117 was a loss-of-function mutation, as expected. The second frameshift at position 659, was, surprisingly, predicted to be a gain-of-function mutation. Additional eVIP Pathways analysis of RNF43 G659fs predicted 10 pathways to be significantly altered, including TNF alpha via NFKB signaling, KRAS signaling, and hypoxia. To validate these predictions, we performed reporter assays and found that all eVIP2 impactful pathways tested in the assay were activated by expression of RNF43 G659fs, but not by expression of RNF43 WT, supporting that RNF43 G659fs is a gain-of-function mutation and its effect on the identified pathways. The eVIP2 method is an important step towards overcoming the current challenge of variant interpretation in the implementation of precision medicine. eVIP2 is available at https://github.com/BrooksLabUCSC/eVIP2.

bioinformatics↗

bioRxiv2019

Phen2Gene: Rapid Phenotype-Driven Gene Prioritization for Rare Diseases

Human Phenotype Ontology (HPO) terms are increasingly used in diagnostic settings to aid in the characterization of patient phenotypes. The HPO annotation database is updated frequently and can provide detailed phenotype knowledge on various human diseases, and many HPO terms are now mapped to candidate causal genes with binary relationships. To further improve the genetic diagnosis of rare diseases, we incorporated these HPO annotations, gene-disease databases, and gene-gene databases in a probabilistic model to build a novel HPO-driven gene prioritization tool, Phen2Gene. Phen2Gene accesses a database built upon this information called the HPO2Gene Knowledgebase (H2GKB), which provides weighted and ranked gene lists for every HPO term. Phen2Gene is then able to access the H2GKB for patient-specific lists of HPO terms or PhenoPackets descriptions supported by GA4GH (http://phenopackets.org/), calculate a prioritized gene list based on a probabilistic model, and output gene-disease relationships with great accuracy. Phen2Gene outperforms existing gene prioritization tools in speed, and acts as a real-time phenotype driven gene prioritization tool to aid the clinical diagnosis of rare undiagnosed diseases. In addition to a command line tool released under the MIT license (https://github.com/WGLab/Phen2Gene), we also developed a web server and web service (https://phen2gene.wglab.org/) for running the tool via web interface or RESTful API queries. Finally, we have curated a large amount of benchmarking data for phenotype-to-gene tools involving 197 patients across 76 scientific articles and 85 patients de-identified HPO term data from CHOP.

bioinformatics↗

bioRxiv2019

Polyadenylation of Histone H3.1 mRNA Promotes Cell Transformation by Displacing H3.3 from Gene Regulatory Elements

Replication-dependent canonical histone messenger RNAs (mRNAs) do not terminate with a poly(A) tail at the 3 end. We previously demonstrated that exposure to arsenic, an environmental carcinogen, induces polyadenylation of canonical histone H3.1 mRNA. The addition of a poly(A) tail to the H3.1 mRNA caused transformation of human cells in vitro, but the underlying mechanisms are unknown. Here we report that polyadenylation of H3.1 mRNA increases H3.1 protein level, resulting in depletion of histone variant H3.3 at active promoters, enhancers, and insulator regions through its displacement. Cells underwent transcriptional deregulation, G2/M cell cycle arrest, chromosome aneuploidy and aberrations. Furthermore, knocking down the expression of H3.3 induced cell transformation, whereas ectopic expression of H3.3 attenuated arsenic-induced cell transformation, suggesting that H3.3 displacement might be central to tumorigenic effects of polyadenylated H3.1 mRNA. Our study provides novel insights into the importance of proper histone stoichiometry in maintaining genome integrity.\n\nHighlightsO_LIPolyadenylation of canonical histone H3.1 mRNA promotes tumor formation in nude mice\nC_LIO_LIHistone variant H3.3 is displaced from critical gene regulatory elements by overexpression of polyadenylated H3.1 mRNA\nC_LIO_LIIncreased polyadenylated H3.1 mRNA causes abnormal transcription, cell cycle arrest, and chromosomal instability\nC_LIO_LIArsenic induces polyadenylation of H3.1 mRNA in vivo\nC_LI

molecular biology↗

bioRxiv2019

GWAS and Fine-Mapping of Livability and Six Disease Traits in Holstein Cattle

BackgroundHealth traits are of significant economic importance to the dairy industry due to their effects on milk production and associated treatment costs. Genome-wide association studies (GWAS) provide a means to identify associated genomic variants and thus reveal insights into the genetic architecture of complex traits and diseases. The objective of this study is to investigate the genetic basis of seven health traits in dairy cattle and to identify potential candidate genes associated with cattle health using GWAS, fine mapping, and analyses of multitissue transcriptome data.\n\nResultsWe studied cow livability and six direct disease traits, mastitis, ketosis, hypocalcemia, displaced abomasum, metritis, and retained placenta, using de-regressed breeding values and more than three million imputed DNA sequence variants. After data edits and filtering on reliability, phenotypes for 11,880 to 24,699 Holstein bulls were included in the analyses of the seven traits. GWAS was performed using a mixed-model association test, and a Bayesian fine-mapping procedure was conducted to calculate a posterior probability of causality to each variant and gene in the candidate regions. The GWAS results detected a total of eight genome-wide significant associations for three traits, cow livability, ketosis, and hypocalcemia, including the bovine MHC region associated with livability. Our fine-mapping of associated regions reported 20 candidate genes with the highest posterior probabilities of causality for cattle health. Combined with transcriptome data across multiple tissues in cattle, we further exploited these candidate genes to identify specific expression patterns in disease-related tissues and relevant biological explanations such as the expression of GC in the liver and association with mastitis as well as the CCDC88C expression in CD8 cells and association with cow livability.\n\nConclusionsCollectively, our analyses report six significant associations and 20 candidate genes of cattle health. With the integration of multi-tissue transcriptome data, our results provide useful information for future functional studies and better understanding of the biological relationship between genetics and disease susceptibility in cattle.

genetics↗

bioRxiv2019

Deep Learning-Based Point-Scanning Super-Resolution Imaging

Point scanning imaging systems (e.g. scanning electron or laser scanning confocal microscopes) are perhaps the most widely used tools for high resolution cellular and tissue imaging. Like all other imaging modalities, the resolution, speed, sample preservation, and signal-to-noise ratio (SNR) of point scanning systems are difficult to optimize simultaneously. In particular, point scanning systems are uniquely constrained by an inverse relationship between imaging speed and pixel resolution. Here we show these limitations can be mitigated via the use of deep learning-based super-sampling of undersampled images acquired on a point-scanning system, which we termed point-scanning super-resolution (PSSR) imaging. Oversampled, high SNR ground truth images acquired on scanning electron or Airyscan laser scanning confocal microscopes were crappified to generate semi-synthetic training data for PSSR models that were then used to restore real-world undersampled images. Remarkably, our EM PSSR model could restore undersampled images acquired with different optics, detectors, samples, or sample preparation methods in other labs. PSSR enabled previously unattainable 2 nm resolution images with our serial block face scanning electron microscope system. For fluorescence, we show that undersampled confocal images combined with a multiframe PSSR model trained on Airyscan timelapses facilitates Airyscan-equivalent spatial resolution and SNR with [~]100x lower laser dose and 16x higher frame rates than corresponding high-resolution acquisitions. In conclusion, PSSR facilitates point-scanning image acquisition with otherwise unattainable resolution, speed, and sensitivity.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=116 SRC=\"FIGDIR/small/740548v8_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (90K):\norg.highwire.dtl.DTLVardef@fbf19aorg.highwire.dtl.DTLVardef@b2cc88org.highwire.dtl.DTLVardef@921e1corg.highwire.dtl.DTLVardef@f6c5af_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2019

Auxin-induced nanoclustering of membrane signaling complexes underlies cell polarity establishment in Arabidopsis

Cell polarity is fundamental to the development of both eukaryotic and prokaryotic organisms, yet the mechanism of its establishment remains poorly understood. Here we show that signal-activated nanoclustering of membrane proteins and a cytoskeleton-based feedback loop provide an important mechanism for the establishment of cell polarity. The phytohormone auxin promoted sterol-dependent nanoclustering of cell surface transmembrane receptor-like kinase 1 (TMK1) to initiate cell polarity during the morphogenesis of Arabidopsis puzzle piece-shaped leaf pavement cells (PC). Auxin-triggered nanoclustering of TMK1 stabilized flotillin-associated ordered nanodomains, which were essential for auxin-mediated formation of ROP6 GTPase nanoclusters that act downstream TMK1 to promote cortical microtubule ordering. Mathematical modeling further demonstrated the essential role of this auxin-mediated stabilization of TMK1 and ROP6 nanoclusters, and predicted the additional requirement of ROP6-dependent cortical microtubules for further stabilization of TMK1-sterol nanodomains and the polarization of PC. This prediction was experimentally validated by genetic and biochemical data. Our studies reveal a new paradigm for polarity establishment: A diffusive signal triggers cell polarization by activating cell surface receptor-mediated lateral segregation of signaling components and a cytoskeleton-mediated positive feedback loop of nanodomain stabilization.\n\nHighlightsO_LISterols are required for cell polarity in Arabidopsis leaf epidermal cells\nC_LIO_LIAuxin promotes lipid ordering and polar distribution of ordered lipid nanodomains at the plasma membrane (PM)\nC_LIO_LIAuxin stabilizes sterol-dependent nanoclustering of transmembrane kinase (TMK1), a PM auxin signal transducer\nC_LIO_LIAuxin-induced TMK1 nanoclustering is required but insufficient for cell polarization\nC_LIO_LIMicrotubule-based feedback stabilization of the auxin-induced TMK1 nanodomains can generate cell polarity\nC_LI

cell biology↗

bioRxiv2019

SOAPTyping: an open-source and cross-platform tool for Sanger sequence-based typing for HLA class I and II alleles

SummaryThe human leukocyte antigen (HLA) gene family plays a key role in the immune response and thus is crucial in many biomedical and clinical settings. Utilizing Sanger sequencing - the gold standard technology for HLA typing - enables accurate identification of HLA alleles with high-resolution. However, there exists a current hurdle that only commercial software such as UType, SBT-Assign and SBTEngine, instead of any open source tools could be applied to perform HLA typing based on Sanger sequencing. To fill the gap, we developed a stand-alone, open-source and cross-platform software, known as SOAPTyping, for Sanger-based typing in HLA class I and II alleles.\n\nAvailability and implementationSOAPTyping is implemented in C++ language and Qt framework, which is supported on Windows, Mac and Linux. Source code and detailed documentation are accessible via the project GitHub page: https://github.com/BGI-flexlab/SOAPTyping.\n\nContactfangl@genomics.cn\n\nSupplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2019

3D observation of large-scale subcellular dynamics in vivo at the millisecond scale

Observing large-scale three-dimensional (3D) subcellular dynamics in vivo at high spatiotemporal resolution has long been a pursuit for biology. However, both the signal-to-noise ratio and resolution degradation in multicellular organisms pose great challenges. Here, we propose a method, termed Digital Adaptive Optics Scanning Lightfield Mutual Iterative Tomography (DAOSLIMIT), featuring both 3D incoherent synthetic aperture and tiled wavefront correction in post-processing. We achieve aberration-free fluorescence imaging in vivo over a 150 x 150 x 16 m3 field-of-view with the spatiotemporal resolution up to 250 nm laterally and 320 nm axially at 100 Hz, corresponding to a huge data throughput of over 15 Giga-voxels per second. Various fast subcellular processes are observed, including mitochondrial dynamics in cultured neurons, membrane dynamics in zebrafish embryos, and calcium propagation in cardiac cells, human cerebral organoids, and Drosophila larval neurons, enabling simultaneous in vivo studies of morphological and functional dynamics in 3D.

cell biology↗