Biology subjects

Chen, T.

Publications and source records attributed to Chen, T..

At least 307 records · Page 17Linked to original sources

bioRxiv2020

Transcriptome analysis reveals the effects of transgenic expression of the Gal4 protein on normal gene expression in silkworm tissues

The Gal4/upstream activating sequence(UAS) system, a well-known genetic tool, has been widely used to analyze gene function in many organisms, including the silkworm (Bombyx mori), a model lepidopteran insect. Several studies have suggested that Gal4 protein activation in tissues can negatively affect transgenic individuals; however, whether and to what extent the Gal4 protein affects normal endogenous gene expression have rarely been studied. Here, we analyzed the transcriptomes of transgenic silkworms expressing the Gal4 protein at high levels in both the wing disc (WD) and epidermis (EP) and investigated gene expression changes in both tissues. Overall, 24,593 genes were identified in the WD and EP libraries, and 2,025 and 2,488 were identified as significant differentially expressed genes(DEGs) in the WD and EP between the transgenic and control groups, respectively. These DEGs were further annotated by gene function classification and pathway assessment using public databases. In addition, 506 DEGs were shared (common) between both tissues. Of these, 97 genes were commonly upregulated, and 234 were commonly downregulated; many of them were annotated to be involved in metabolic processes such as "fat digestion and absorption", "glycine, serine and threonine metabolism" and "glutathione metabolism" and in signal transduction pathways such as the "Rap1 signaling pathway", "MAPK signaling pathway" and "Hippo signaling pathway". Overall, this work enhances understanding of the effects of transgenic Gal4 protein expression on normal gene expression in silkworm tissues and suggests that researchers should pay attention to unexpected effects when using the Gal4/UAS system to study gene function.

genomics↗

bioRxiv2020

A mathematical model for simulating the transmission of Wuhan novel Coronavirus

As reported by the World Health Organization, a novel coronavirus (2019-nCoV) was identified as the causative virus of Wuhan pneumonia of unknown etiology by Chinese authorities on 7 January, 2020. In this study, we developed a Bats-Hosts-Reservoir-People transmission network model for simulating the potential transmission from the infection source (probable be bats) to the human infection. Since the Bats-Hosts-Reservoir network was hard to explore clearly and public concerns were focusing on the transmission from a seafood market (reservoir) to people, we simplified the model as Reservoir-People transmission network model. The basic reproduction number (R0) was calculated from the RP model to assess the transmissibility of the 2019-nCoV.

systems biology↗

bioRxiv2020

The highly expressed lipid buffer FABP4 enforces adipocyte cell identity by driving the initial cell differentiation process

How progenitor cells can attain a distinct differentiated cell identity is a challenging problem given that critical transcription factors are often not unique to a differentiation process and the fluctuating signaling environment in which cells exist. Here we test the hypothesis that a unique differentiated cell identity can result from a core component of the differentiated state doubling up as a signaling protein that also drives differentiation. Using live single-cell imaging in the adipocyte differentiation system, we show that progenitor fat cells (preadipocytes) can only commit to terminally differentiate after upregulating FABP4, a lipid buffer that is highly enriched in mature adipocytes. Upon induction of adipogenesis, we show that after a long delay, cells first abruptly start to engage a positive feedback between CEBPA and PPARG before then engaging, after a second delay, a positive feedback between FABP4 and PPARG. These sequential positive feedbacks both need to engage in order to drive PPARG levels past the threshold for irreversible differentiation. In the last step before commitment, PPARG transcriptionally increases FABP4 expression while fatty-acid loaded FABP4 binds to and increases PPARG activity. Together, our study suggests a control principle for robust cell identity whereby a core component of the differentiated state also promotes differentiation from its own progenitor state. HIGHLIGHTSO_LIFatty-acid loaded FABP4 binds to and increases PPARG expression, thereby turning on PPARG positive feedback loops that further increase PPARG expression. C_LIO_LIFABP4 critically controls the second phase of adipogenesis between activation of the feedback loops and reaching the threshold to differentiate. C_LIO_LIOnly a small fraction ([~]10%) of the FABP4 levels typically attained in mature fat cells is needed to commit cells to the differentiated state, thus providing an explanation for why maintenance of the mature adipocyte state is so robust. C_LI

cell biology↗

bioRxiv2019

A mathematical model exhibiting the effect of DNA methylation on the stability boundary in cell-fate networks

Cell-fate networks are traditionally studied within the framework of gene regulatory networks. This paradigm considers only interactions of genes through expressed transcription factors and does not incorporate chromatin modification processes. This paper introduces a mathematical model that seamlessly combines gene regulatory networks and DNA methylation, with the goal of quantitatively characterizing the contribution of epigenetic regulation to gene silencing. The "Basin of Attraction percentage" is introduced as a metric to quantify gene silencing abilities. As a case study, a computational and theoretical analysis is carried out for a model of the pluripotent stem cell circuit as well as a simplified self-activating gene model. The results confirm that the methodology quantitatively captures the key role that methylation plays in enhancing the stability of the silenced gene state.

systems biology↗

bioRxiv2019

Emergence of single cell mechanical behavior and polarity within epithelial monolayers drives collective cell migration

The directed migration of cell collectives is essential in various physiological processes, such as epiboly, intestinal epithelial turnover, and convergent extension during morphogenesis as well as during pathological events like wound healing and cancer metastasis1,2. Collective cell migration leads to the emergence of coordinated movements over multiple cells. Our current understanding emphasizes that these movements are mainly driven by large-scale transmission of signals through adherens junctions3,4. In this study, we show that collective movements of epithelial cells can be triggered by polarity signals at the single cell level through the establishment of coordinated lamellipodial protrusions. We designed a minimalistic model system to generate one-dimensional epithelial trains confined in ring shaped patterns that recapitulate rotational movements observed in vitro in cellular monolayers and in vivo in genitalia or follicular cell rotation5-7. Using our system, we demonstrated that cells follow coordinated rotational movements after the establishment of directed Rac1-dependent polarity over the entire monolayer. Our experimental and numerical approaches show that the maintenance of coordinated migration requires the acquisition of a front-back polarity within each single cell but does not require the maintenance of cell-cell junctions. Taken together, these unexpected findings demonstrate that collective cell dynamics in closed environments as observed in multiple in vitro and in vivo situations5,6,8,9 can arise from single cell behavior through a sustained memory of cell polarity.

biophysics↗

bioRxiv2019

Geldanamycin inhibits Jumonji histone lysine demethylase KDM4 and targets chimeric transcription factor PAX3-FOXO1

Histone lysine demethylases (KDMs) are emerging as therapeutic targets in cancer. Development of potent KDM inhibitors may provide additional options for epigenomics-oriented therapies. Using a Time-Resolved Fluorescence Resonance Energy Transfer (TR-FRET) functional demethylation assay, in combination with a high-content immunofluorescence imaging phenotypic screen, Matrix-Assisted Laser Desorption/Ionization-Fourier Transform Ion Cyclotron Resonance mass spectrometry (MALDI-FTICR MS) and Amplified Luminescent Proximity Homogeneous Assay (ALPHA), we identified geldanamycin, an inhibitor of heat shock protein 90 (Hsp90), as a novel inhibitor of JmjC-domain containing demethylases such as KDM4B. We further found that geldanamycin can destabilize the PAX3-FOXO1 fusion oncoprotein, an Hsp90 client, which is a driver of clinically unfavorable alveolar rhabdomyosarcoma (aRMS). We then hypothesized that dual inhibition of PAX3-FOXO1 and epigenetic modifiers of aRMS would have synergistic antitumor activity. We repurposed the geldanamycin analog 17-DMAG to target aRMS and found that 17-DMAG significantly delays tumor growth, extends survival in xenograft mouse models, and inhibits expression of PAX3-FOXO1 targets and multiple oncogenic pathways including MYC, E2F and NOTCH. In addition, the combination of 17-DMAG with conventional chemotherapy or the bromodomain inhibitor JQ1 significantly enhances therapeutic efficacy. In summary, we have identified geldanamycin and 17-DMAG as dual KDM/Hsp90 inhibitors and 17-DMAG is efficacious against PAX3-FOXO1-driven rhabdomyosarcoma.

cancer biology↗

bioRxiv2019

Towards Practical and Robust DNA-based Data Archiving by Codec System Named ‘Yin-Yang’

DNA is a promising data storage medium due to its remarkable durability and space-efficient storage. Early bit-to-base transcoding schemes have primarily pursued information density, at the expense however of introducing biocompatibility challenges or at the risk of decoding failure. Here, we propose a robust transcoding algorithm named the "Yin-Yang Codec" (YYC), using two rules to encode two binary bits into one nucleotide, to generate DNA sequences highly compatible with synthesis and sequencing technologies. We encoded two representative file formats and stored them in vitro as 200-nt oligo pools and in vivo as an ~54-kb DNA fragment in yeast cells. Sequencing results show that YYC exhibits high robustness and reliability for a wide variety of data types, with an average recovery rate of 99.94% at 104 molecule copies and an achieved recovery rate of 87.53% at 100 copies. In addition, the in vivo storage demonstration achieved for the first time an experimentally measured physical information density of 198.8 EB per gram of DNA (44% of the theoretical maximum for DNA).

synthetic biology↗

bioRxiv2019

Genomic profiling of circulating tumor DNA reveals genetics and residual disease in NK/T lymphoma

BackgroundExtranodal NK/T-cell lymphoma, nasal type (ENTKL), is an aggressive hematological malignancy with poor prognosis. Early detection of tumors at initial diagnosis or during routine surveillance is important for improving survival outcomes. Molecular profiling of circulating tumor DNA (ctDNA) is a promising noninvasive tool for monitoring disease status. Here, we investigated the feasible of ctDNA detection in ENTKL. MethodsPlasma ctDNA was assessment were based on blood specimens that were collected from 65 patients recently diagnosed with ENKTL at the hematology medical center of Xinqiao Hospital, longitudinal samples collected under chemotherapy also included. Gene mutation spectrum of ENKTL was analyzed via cancer personalized profiling sequencing (CAPP-Seq). This study is registered with ClinicalTrials.gov (ChiCTR1800014813) ResultsFrom February 2017 to September 2019, 65 patients were enrolled, we found that the most frequently mutated genes were KMT2D (23.1%), APC (12.3%), ATM (10.8%), ASXL3 (9.2%), JAK3 (9.2%), SETD2 (9.2%), TP53 (9.2%), NOTCH1 (7.7%). The mutation frequencies of KMT2D was significantly higher in stage III-IV, and mutations in KMT2D, ASXL3 and JAK3 were significantly correlated with the metabolic tumor burden of the patients. Compared with tumor tissue DNA, ctDNA profiling showed good concordance. Serial ctDNA analysis showed that treatment with chemotherapy could decrease the number and mutation allele frequency of genes. Compared with PET/CT, ctDNA has more advantages for tracking residual disease in patients. In addition, we also found that mutated KMT2D predicted poor prognosis in patients. ConclusionCollectively, our results provide evidence that ctDNA may serve as a novel precision medicine biomarker in ENKTL.

genomics↗

bioRxiv2019

Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

BackgroundThe low cost of 16S rRNA gene sequencing facilitates population-scale molecular epidemiological studies. Existing computational algorithms can parse 16S rRNA gene sequences to high-resolution Amplicon Sequence Variants (ASVs), which represent consistent labels comparable across studies. Assigning these ASVs to species-level taxonomy strengthens the ecological and/or clinical relevance of 16S rRNA gene-based microbiota studies and further facilitates data comparison across studies. ResultsTo achieve this, we developed a broadly applicable method for constructing high-resolution training sets based on the phylogenic relationships among microbes found in a habitat of interested. When used with the naive Bayesian Ribosomal Database Project (RDP) Classifier, this training set achieved species/supraspecies-level taxonomic assignment of 16S rRNA gene-derived ASVs. The key steps for generating such a training set are: 1) constructing an accurate and comprehensive phylogenetic-based, habitat-specific database; 2) compiling multiple 16S rRNA gene sequences to represent the natural sequence variability of each taxon in the database; 3) trimming the training set to match the sequenced regions, if necessary; and 4) placing species sharing closely related sequences into a supraspecies taxonomic level to preserve subgenus-level resolution. As proof of principle, we developed a V1-V3 region training set for the bacterial microbiota of the human aerodigestive tract using the full-length 16S rRNA gene reference sequences compiled in our expanded Human Oral Microbiome Database (eHOMD). We also overcame technical limitations to successfully use Illumina sequences for the 16S rRNA gene V1-V3 region, the most informative segment for classifying bacteria native to the human aerodigestive tract. Finally, we generated a full-length eHOMD 16S rRNA gene training set, which we used in conjunction with an independent PacBio Single Molecule, Real-Time (SMRT)-sequenced sinonasal dataset to validate the representation of species in our training set. This also established the effectiveness of a full-length training set for assigning taxonomy of long-read 16S rRNA gene datasets. ConclusionHere, we present a systematic approach for constructing a phylogeny-based, high-resolution, habitat-specific training set that permits species/supraspecies-level taxonomic assignment to short- and long-read 16S rRNA gene-derived ASVs. This advancement enhances the ecological and/or clinical relevance of 16S rRNA gene-based microbiota studies.

microbiology↗

bioRxiv2019

Genome-wide quantitative trait loci mapping on Verticilliumw

Cotton Verticillium wilt (VW) is a devastating disease seriously affecting fiber yield and quality, and the most effective and economical prevention measure at present is selection and extension of Gossypium varieties harboring high resistant VW. However, multiple attempts to improve the VW resistance of the most widely cultivated Upland cotton have brought in little significant progress, and it seems necessary and urgent to develop Chromosome segment substitution lines (CSSLs) for merging the superior genes related with high yield and wide adaptation from G. hirsutum and VW resistance and excellent fiber quality from G. barbadense. In this study, 300 CSSLs were chosen from the developed BC5F3:5 CSSLs constructed by G. hirsutum CCRI36 and G. barbadense Hai1 to conduct quantitative trait locus (QTL) mapping on VW resistance, and a total of 53 QTLs relevant to VW disease index (DI) were identified together with the phenotypic data of 2 years investigations in two fields with two replications per year. All the QTLs were distributed on 20 chromosomes with phenotypic variation of 3.74-11.89%, of which 29 stable ones were consistent in at least two environments. Based on Meta-analysis on the 53 QTLs, 43 novel ones were identified, while 10 ones consistent to previously identified QTLs. Meanwhile, 32 QTL hotspot regions were detected, including 15 ones were novel. This study concentrates on QTL identification and screening hotspot region related with VW in the 300 CSSLs, which lay a solid platform not only for revealing the genetic and molecular mechanisms of VW resistance, but also for further fine mapping, gene cloning and molecular designing in breeding program for resistant cotton varieties.

plant biology↗

bioRxiv2019

Gels for Live Analysis of Compartmentalized Environments (GLAnCE): A Tissue Model to Probe Tumour Phenotypes at Tumour-Stroma Interfaces

The interface between a tumour and the adjacent stroma is a site of great importance for tumour development. At this site, carcinoma cells are highly proliferative, undergo invasive phenotypic changes, and directly interact with surrounding stromal cells, such as cancer-associated fibroblasts (CAFs) which further exert pro-tumorigenic effects. Here we describe the development of GLAnCE (Gels for Live Analysis of Compartmentalized Environments), an easy-to-use hydrogel-culture platform for investigating CAF-tumour cell interaction dynamics in vitro at a tumour-stroma interface. GLAnCE enables observation of CAF-mediated enhancement of both tumour cell proliferation and invasion at the tumour-stroma interface in real time, as well as stratification between phenotypes at the interface versus in the bulk tumour tissue compartment. We found that CAF presence resulted in the establishment of an invasion-permissive, interface-specific matrix environment, that leads to carcinoma cell movement outwards from the tumour edge and tumour cell invasion. Furthermore, the spatial stratification capability of GLAnCE was leveraged to discern differences between tumour cell epithelial-to-mesenchymal (EMT) transition genes induced by paracrine signaling from CAFs versus genes induced by interface-specific, CAF-mediated microenvironment. GLAnCE combines high usability and tissue complexity, to provide a powerful in vitro platform to probe mechanisms of tumour cell movement specific to the microenvironment at the tumour-stroma interface.

bioengineering↗

bioRxiv2019

The Acute Myeloid Leukemia variant DNMT3A Arg882His is a DNMT3B-like enzyme

Mutations in DNMT3A, particularly the Arg882His substitution is highly prevalent in acute myeloid leukemia. Although the reduced activity of DNMT3A Arg882His variant alters DNA methylation, the underlying cause of its oncogenic effect is not fully understood. Our data show that DNMT3A Arg882His variant acquires CpG flanking sequence preference highly similar to that of DNMT3B. Interestingly, a similar substrate preference was observed in DNMT3A WT enzyme upon the loss of cooperative kinetic mechanism. We tested if DNMT3A Arg882His could preferably methylate DNMT3B-specific target sites. Rescue experiments in Dnmt3a/3b double knockout mouse embryonic stem cells show that the corresponding Arg878His mutation in mouse DNMT3A severely impairs its ability to methylate major satellite DNA, a DNMT3A-preferred target, but has no overt effect on the ability to methylate minor satellite DNA, a DNMT3B-preferred target. Our data suggest that methylation of DNMT3B target sites by DNMT3A Arg882His variant could contribute to its oncogenic potential.

biochemistry↗

bioRxiv2019

Collagen Production and Niche Engineering: A Novel Strategy for Cancer Cells to Survive Acidosis and Evolve

Ductal Carcinoma in situ (DCIS) is an avascular disease characterized by profound acidosis. Pre-malignant cells within this niche must adapt to acidosis to survive and thrive. A component of this acid-adaptation involves extracellular matrix remodeling leading to niche construction and remodeling. Using discovery proteomics, we identified that collagen producing enzyme PLODs are upregulated in acid-adapted breast cancer cells. Second harmonic generation microscopy showed significant collagen deposition within DCIS lesions of patients. In vitro analyses identified that acid-adaptation involves production of rare collagens that can be regulated by Ras and SMAD pathway. Secretome analysis showed upregulation ECM remodeling enzymes such as TGM2 and LOXL2. Comparison of acid induced collagens in vitro and in patient data showed correlation between rare collagens production and survival of patients. We conclude acidosis induces collagen production by cancer cells and promote growth independent of basal membrane attachment. The independently produced collagen can be used for niche construction and engineering as an adaptation strategy of cancer cells to survive and evolve.

cancer biology↗

bioRxiv2019

Transcription factor NF-κB in a basal metazoan, the sponge, has conserved and unique sequences, activities, and regulation

Biological and biochemical functions of immunity transcription factor NF-{kappa}B in basal metazoans are largely unknown. Herein, we characterize transcription factor NF-{kappa}B from the demosponge Amphimedon queenslandica (Aq), in the phylum Porifera. Structurally and phylogenetically, the Aq-NF-{kappa}B protein is most similar to NF-{kappa}B p100 and p105 among vertebrate proteins, with an N-terminal DNA-binding/dimerization domain, a C-terminal Ankyrin (ANK) repeat domain, and a DNA binding-site profile more similar to human NF-{kappa}B proteins than Rel proteins. Aq-NF-{kappa}B also resembles the mammalian NF-{kappa}B protein p100 in that C-terminal truncation results in translocation of Aq-NF-{kappa}B to the nucleus and increases its transcriptional activation activity. Overexpression of a human or sea anemone I{kappa}B kinase (IKK) can induce C-terminal processing of Aq-NF-{kappa}B in vivo, and this processing requires C-terminal serine residues in Aq-NF-{kappa}B. Unlike human NF-{kappa}B p100, however, the C-terminal sequences of Aq-NF-{kappa}B do not effectively inhibit its DNA-binding activity when expressed in human cells. Tissue of another demosponge, a black encrusting sponge, contains NF-{kappa}B site DNA-binding activity and an NF-{kappa}B protein that appears mostly processed and in the nucleus of cells. NF-{kappa}B DNA-binding activity and processing is increased by treatment of sponge tissue with LPS. By transcriptomic analysis of A. queenslandica we identified likely homologs to many upstream NF-{kappa}B pathway components. These results present a functional characterization of the most ancient metazoan NF-{kappa}B protein to date, and show that many characteristics of mammalian NF-{kappa}B are conserved in sponge NF-{kappa}B, but the mechanism by which NF-{kappa}B functions and is regulated in the sponge may be somewhat different.

cell biology↗

bioRxiv2019

MMCA: a Web-based Server for the Microbiome and Metabolome Correlation Analysis

BackgroundIn the last decade, integrative studies of microbiome and metabolome have experienced exponential growth in understanding their impact on human health and diseases. However, analyzing the resulting multi-omics data and their correlations remains a significant challenge in current studies due to the lack of a comprehensive computational tool to facilitate data integration and interpretation. In this study, we have developed a microbiome and metabolome integrative analysis pipeline (M2IA) to meet the urgent needs for tools that effectively integrate microbiome and metabolome data to derive biological insights.\n\nResultsM2IA streamlines the integrative data analysis between metabolome and microbiome, including both univariate analysis and multivariate modeling methods. KEGG-based functional analysis of microbiome and metabolome are provided to explore their biological interactions within specific metabolic pathways. The functionality of M2IA was demonstrated using TwinsUK cohort data with 1116 fecal metabolites and 16s rRNA microbiome from 786 individuals. As a result, we identified two important pathways, i.e., the benzoate degradation and phosphotransferase system, were closely associated with obesity from both metabolome and microbiome.\n\nConclusionsM2IA is a public available web server (http://m2ia.met-bioinformatics.cn) with the capability to investigate the complex interplay between microbiome and metabolome, and help users to develop mechanistic hypothesis for nutritional and personalized therapies of diseases.

bioinformatics↗

bioRxiv2019

The relative transmissibility of shigellosis among male and female individuals in Hubei Province, China: a modelling study

ObjectiveShigellosis has been a heavy burden in China. However, its relative transmissibility in male and female individuals remains unclear.\n\nMethodA sex-based Susceptible-Exposed-Infectious/Asymptomatic-Recovered (SEIAR) model was applied to explore the dataset of reported shigellosis cases built by Hubei Province from 2005 to 2017. Two indicators, secondary attack rate (SAR) and relative ratio of SAR between males and females, were developed to assess the relative transmissibility in males and females.\n\nResultsThe number of cases and reported incidences in males and females demonstrated a significant decreasing trend (Male trend:{chi} 2 = 11.268, P = 0.001, Female trend:{chi} 2 = 11.144, P = 0.001). SEIAR model had a great fitting effect with the data of shigellosis (P < 0.001). Our simulation revealed that, when parameter {beta}fm = 0, the greatest decrease in cases were obtained for different genders. The median value for SARmm was 2.3225 x 10-8 (Range: 1.7574 x 10-8 - 3.8565 x 10-8), SARmf was 2.5729 x 10-8 (Range: 1.3772 x 10-8 - 3.2773 x 10-8), SARfm was 2.7630 x 10-8 (Range: 1.8387 x 10-8 - 4.2638 x 10-8) and SARff was 2.1061 x 10-8 (Range: 1.0201 x 10-8 - 3.2140 x 10-8). The median value of relative ratio calculated by SAR in mm versus (vs) mf was 0.93 (Range: 0.75 - 1.47), mm vs fm was 0.90 (Range: 0.41 - 1.81), mm vs ff was 1.07 (Range: 0.55 - 2.93), mf vs fm was 0.99 (Range: 0.32 - 1.25), mf vs ff was 1.17 (Range: 0.43 - 3.21) and ff vs fm was 0.75 (Range: 0.35 - 1.06).\n\nConclusionTransmissibility of shigellosis is different among male and female individuals. Shigellosis seems to be more transmissible in males than in females.\n\nAuthor summaryShigellosis, also known as bacillary dysentery, is an infectious disease caused by the genus Shigella spp. Developing countries have high disease burden of shigellosis. However, its relative transmissibility in male and female individuals remains unclear. In this study, we employed a mathematical model to explore the dataset of reported shigellosis cases built by Hubei Province, China from 2005 to 2017. Two indicators, secondary attack rate (SAR) and relative ratio of SAR between males and females, were developed to assess the relative transmissibility in males and females. We found that shigellosis has medium transmissibility among male and female individuals. The disease seems to be more transmissible in males than in females.

epidemiology↗

bioRxiv2019

Simulation-based comparison of Biopharmaceutics Classification System and drug structure

BackgroundThe Biopharmaceutics Classification System (BCS), which classifies bioactive molecules based on solubility and permeability, is widely used to guide new drug development and drug formulation, as well as predict pharmacokinetics. Here we performed computer simulations to study correlations between a molecules structure and its BCS classification.\n\nMethodsA total of 411 small molecules were assigned to BCS categories based on published drug data, and their Pybel-FP4 fingerprints were extrapolated. The information gain(IG) of each fingerprint was calculated and its characteristic structure analyzed. IG was calculated using multiple thresholds, and results were verified using support vector machine prediction, while taking into account the dose coefficient(0-0.1, 0.1-1, or>1). Structural functional features common to fingerprints of compounds in each type of BCS class were determined using computer simulations.\n\nResultsBCS classes III and IV appear to share several structural and functional characteristics, including Secondary aliphaticamine, Michael_acceptor, Isothiourea, and Sulfonamide Sulfonic_derivatives.\n\nConclusionWe demonstrate that our approach can correlate characteristic fingerprints of small-molecule drugs with BCS classifications, which may help guide the development and optimization of new drugs.

molecular biology↗

bioRxiv2019

Volumetric two-photon imaging in live cells and embryos via axially gradient excitation

Two-photon microscopy(TPM) that features subcellular resolution, intrinsic optical sectioning ability, and deep penetration in sample is a powerful tool of bioimaging. However, the process of layer-by-layer scanning to form a 3D image inherently limits the volumetric imaging speed and significantly increases the phototoxicity. Here we develop a gradient TPM technique that enables rapid volumetric imaging by only acquiring two 2D images. By sequentially exciting the specimen with two axially elongated two-photon beams with complementary gradient intensities, the axial positions of fluorophores can be decoded from the intensity ratio of the paired images. We achieve an axial localization accuracy of 0.728 {+/-} 0.657 m, which is sufficient for rapid 3D subcellular imaging. We demonstrate the flexibility of the gradient TPM on a variety of sparsely labelled samples, including bead phantoms, mouse brain tissues, live macrophages and live nematode embryos. The results show that, compared with conventional TPM, the 3D imaging speed increases 6 folds while the photobleaching and photodamage are extremely reduced.

bioengineering↗