Biology subjects

Chen, W.

Publications and source records attributed to Chen, W..

624 records · Page 35Linked to original sources

bioRxiv2017

Rapid DNA Replication Origin Licensing Protects Stem Cell Pluripotency

Complete and robust human genome duplication requires loading MCM helicase complexes at many DNA replication origins, an essential process termed origin licensing. Licensing is restricted to G1 phase of the cell cycle, but G1 length varies widely among cell types. Using quantitative single cell analyses we found that pluripotent stem cells with naturally short G1 phases load MCM much faster than their isogenic differentiated counterparts with long G1 phases. During the earliest stages of differentiation towards all lineages, MCM loading slows concurrently with G1 lengthening, revealing developmental control of MCM loading. In contrast, ectopic Cyclin E overproduction uncouples short G1 from fast MCM loading. Rapid licensing in stem cells is caused by accumulation of the MCM loading protein, Cdt1. Prematurely slowing MCM loading in pluripotent cells not only lengthens G1 but also accelerates differentiation. Thus, rapid origin licensing is an intrinsic characteristic of stem cells that contributes to pluripotency maintenance.

cell biology↗

bioRxiv2017

Dependence of Intravoxel Incoherent Motion MR threshold b-value selection for separating perfusion and diffusion compartment and liver fibrosis diagnostic performance.

PurposeTo explore how the selection of threshold b-value impacts Intravoxel Incoherent Motion (IVIM) diffusion parameters of PF (f), Dslow (D),and Dfast (D*) values and their performance for liver fibrosis detection.\n\nMaterials and MethodsFifteen healthy volunteers and 33 hepatitis-b patients were included. With a 1.5 T MR scanner and respiration gating, IVIM data was acquired with 10 b-values of 10,20,40,60,80,100,150, 200, 400, and 800 s/mm2. Signal measurement was performed on right liver. Segmented-unconstrained analysis was used to compute IVIM parameters, and six threshold b-values between 40 and 200 s/mm2 were compared. PF, Dslow, and Dfast values were placed along the x-axis, y-axis, and z-axis, and a plane was defined to separate volunteers from patients.\n\nResultsHigher threshold b-values were associated with higher PF measurement; while lower threshold b-values led to higher Dslow and Dfast measurements. The dependence of PF, Dslow, and Dfast on threshold b-value differed between healthy livers and fibrotic livers; with the healthy livers showing a higher dependence. Threshold b-value=60 s/mm2 showed the largest mean distance between healthy liver datapoints vs. fibrotic liver datapoints in 3-dimensional space.\n\nConclusionFor segmented-unconstrained analysis, the selection of threshold b-value=60 s/mm2 improves IVIM diffusion differentiation between healthy livers and fibrotic livers.

biophysics↗

bioRxiv2017

Resequencing the Escherichia coli genome by GenoCare single molecule sequencing platform

Next generation sequencing (NGS) has revolutionized life sciences research. Recently, a new class of third-generation sequencing platforms has arrived to meet increasing demands in the clinic, capable of directly measuring DNA and RNA sequences at the single-molecule level without amplification. Here, we use the new GenoCare single molecule sequencing platform from Direct Genomics to resequence the E. coli genome and show comparable performance to the Illumina MiSeq system. Our platform detects single-molecule fluorescence by total internal reflection microscopy, with sequencing-by-synthesis chemistry. With a consensus sequence of 99.71% nucleotide identity to that of the Illumina MiSeq systems, GenoCare was determined to be a reliable platform for single-molecule sequencing, with strong potential for clinical applications.

genomics↗

bioRxiv2017

Virtual Reality system for freely-moving rodents.

Spatial navigation, active sensing, and most cognitive functions rely on a tight link between motor output and sensory input. Virtual reality (VR) systems simulate the sensorimotor loop, allowing flexible manipulation of enriched sensory input. Conventional rodent VR systems provide 3D visual cues linked to restrained locomotion on a treadmill, leading to a mismatch between visual and most other sensory inputs, sensory-motor conflicts, as well as restricted naturalistic behavior. To rectify these limitations, we developed a VR system (ratCAVE) that provides realistic and low-latency visual feedback directly to head movements of completely unrestrained rodents. Immersed in this VR system, rats displayed naturalistic behavior by spontaneously interacting with and hugging virtual walls, exploring virtual objects, and avoiding virtual cliffs. We further illustrate the effect of ratCAVE-VR manipulation on hippocampal place fields. The newly-developed methodology enables a wide range of experiments involving flexible manipulation of visual feedback in freely-moving behaving animals.

animal behavior and cognition↗

bioRxiv2017

Deep Residual Network Reveals a Nested Hierarchy of Distributed Cortical Representation for Visual Categorization

The brain represents visual objects with topographic cortical patterns. To address how distributed visual representations enable object categorization, we established predictive encoding models based on a deep residual neural network, and trained them to predict cortical responses to natural movies. Using this predictive model, we mapped human cortical representations to 64,000 visual objects from 80 categories with high throughput and accuracy. Such representations covered both the ventral and dorsal pathways, reflected multiple levels of object features, and preserved semantic relationships between categories. In the entire visual cortex, object representations were modularly organized into three categories: biological objects, non-biological objects, and background scenes. In a finer scale specific to each module, object representations revealed sub-modules for further categorization. These findings suggest that increasingly more specific category is represented by cortical patterns in progressively finer spatial scales. Such a nested hierarchy may be a fundamental principle for the brain to categorize visual objects with various levels of specificity, and can be explained and differentiated by object features at different levels.

neuroscience↗

bioRxiv2017

A Combined Use Of Intravoxel Incoherent Motion MRI Parameters Can Differentiate Early Stage Hepatitis-B Fibrotic Livers From Healthy Livers

This study investigated a combined use of IVIM parameters Dslow (D), PF (f) and Dfast (D*) for liver fibrosis evaluation. 16 healthy volunteers (F0) and 33 hepatitis-b patients (stage F1= 15, stage F2-4 = 18) were included. With a 1.5-T MR scanner and respiration-gating, IVIM diffusion weighted imaging was acquired using a single-shot echo-planar imaging sequence with ten b-values of 10, 20, 40, 60, 80, 100, 150, 200, 400, and 800 s/mm2. Signal measurement was performed on right liver parenchyma. With a 3-dimensional tool, Dslow, PF, and Dfast values were placed along the x-axis, y-axis, and z-axis, and a plane was defined to separate healthy volunteers from patients. 3-dimensional tool demonstrated healthy volunteers and all patients with liver fibrosis could be separated. Classification and Regression Tree showed a combination of PF (PF < 12.55%), Dslow (Dslow < 1.152 x10-3 mm2/s) and Dfast (Dfast <13.36 x10-3 mm2/s) could differentiate healthy subjects and all fibrotic livers (F1-F4) with an area under the curve of logistic regression (AUC) of 0.986. The AUC for differentiation of healthy livers vs. F2-4 livers was 1. PF offered the best diagnostic value, followed by Dslow; however, all three parameters of PF, Dslow, and Dfast contributed to liver fibrosis detection.

biophysics↗

bioRxiv2017

Extending Chemical Perturbations Of The Ubiquitin Fitness Landscape In A Classroom Setting

Although the primary protein sequence of ubiquitin (Ub) is extremely stable over evolutionary time, it is highly tolerant to mutation during selection experiments performed in the laboratory. We have proposed that this discrepancy results from the difference between fitness under laboratory culture conditions and the selective pressures in changing environments over evolutionary time scales. Building on our previous work (Mavor et al 2016), we used deep mutational scanning to determine how twelve new chemicals (3-Amino-1,2,4-triazole, 5-fluorocytosine, Amphotericin B, CaCl2, Cerulenin, Cobalt Acetate, Menadione, Nickel Chloride, p-fluorophenylalanine, Rapamycin, Tamoxifen, and Tunicamycin) reveal novel mutational sensitivities of ubiquitin residues. We found sensitization of Lys63 in eight new conditions. In total, our experiments have uncovered a sensitizing condition for every position in Ub except Ser57 and Gln62. By determining the Ubiquitin fitness landscape under different chemical constraints, our work helps to resolve the inconsistencies between deep mutational scanning experiments and sequence conservation over evolutionary timescales.\n\nBuilds onMavor D, Barlow KA, Thompson S, Barad BA, Bonny AR, Cario CL, Gaskins G, Liu Z, Deming L, Axen SD, Caceres E, Chen W, Cuesta A, Gate R, Green EM, Hulce KR, Ji W, Kenner LR, Mensa B, Morinishi LS, Moss SM, Mravic M, Muir RK, Niekamp S, Nnadi CI, Palovcak E, Poss EM, Ross TD, Salcedo E, See S, Subramaniam M, Wong AW, Li J, Thorn KS, Conchuir SO, Roscoe BP, Chow ED, DeRisi JL, Kortemme T, Bolon DN, Fraser JS. Determination of Ubiquitin Fitness Landscapes Under Different Chemical Stresses in a Classroom Setting. eLife. 2016.\n\nImpact StatementWe organized a project-based course that used deep mutational scanning in multiple chemical conditions to resolve the inconsistencies between tolerance to mutations in laboratory conditions and sequence conservation over evolutionary timescales.

bioinformatics↗

bioRxiv2017

PHATE: A Dimensionality Reduction Method for Visualizing Trajectory Structures in High-Dimensional Biological Data

With the advent of high-throughput technologies measuring high-dimensional biological data, there is a pressing need for visualization tools that reveal the structure and emergent patterns of data in an intuitive form. We present PHATE, a visualization method that captures both local and global nonlinear structure in data by an information-geometric distance between datapoints. We perform extensive comparison between PHATE and other tools on a variety of artificial and biological datasets, and find that it consistently preserves a range of patterns in data including continual progressions, branches, and clusters. We define a manifold preservation metric DEMaP to show that PHATE produces quantitatively better denoised embeddings than existing visualization methods. We show that PHATE is able to gain unique insight from a newly generated scRNA-seq dataset of human germ layer differentiation. Here, PHATE reveals a dynamic picture of the main developmental branches in unparalleled detail, including the identification of three novel subpopulations. Finally, we show that PHATE is applicable to a wide variety of datatypes including mass cytometry, single-cell RNA-sequencing, Hi-C, and gut microbiome data, where it can generate interpretable insights into the underlying systems.

bioinformatics↗

bioRxiv2017

Dynamic response to initial stage blindness in visual system development

Sensitive periods and experience-dependent plasticity have become core issues in visual system development. Converging evidence indicates that visual experience is an indispensable factor in establishing mature visual system circuitry during sensitive periods and the visual system exhibits substantial plasticity when facing deprivation. The mechanisms that underlie the environmental regulation of visual system development and plasticity are of great interest but need further exploration. Here, we investigated a unique sample of human infants who experienced initial stage blindness (beginning at birth and lasting 2 to 8 months) before the removal of bilateral cataracts. Retinal thickness, axial length, refractive status, visual grating acuity and genetic integrity were recorded during the preoperative period or at surgery, and then during follow-up. The results showed that the development of the retina is malleable and associated with external environment influences. Our work supported that the retina might play critical roles in the development of the experience-dependent visual system and its malleability might partly contribute to the sensitive period plasticity.\n\nSUMMARY STATEMENTThe follow-up investigation of a group of human infants, who experienced initial stage blindness before the removal of bilateral cataracts, revealed that retinal development is associated with environment influences and its malleability might be a potential basis of plasticity.

developmental biology↗

bioRxiv2017

Scaling single cell transcriptomics through split pool barcoding

Constructing an atlas of cell types in complex organisms will require a collective effort to characterize billions of individual cells. Single cell RNA sequencing (scRNA-seq) has emerged as the main tool for characterizing cellular diversity, but current methods use custom microfluidics or microwells to compartmentalize single cells, limiting scalability and widespread adoption. Here we present Split Pool Ligation-based Transcriptome sequencing (SPLiT-seq), a scRNA-seq method that labels the cellular origin of RNA through combinatorial indexing. SPLiT-seq is compatible with fixed cells, scales exponentially, uses only basic laboratory equipment, and costs one cent per cell. We used this approach to analyze 109,069 single cell transcriptomes from an entire postnatal day 5 mouse brain, providing the first global snapshot at this stage of development. We identified 13 main populations comprising different types of neurons, glia, immune cells, endothelia, as well as types in the blood-brain-barrier. Moreover, we resolve substructure within these clusters corresponding to cells at different stages of development. As sequencing capacity increases, SPLiT-seq will enable profiling of billions of cells in a single experiment.

genomics↗

bioRxiv2017

Complex interactions in legume/cereal intercropping system : role of root exudates in root-to-root communication

Dear Editor,\n\nLegume/cereal intercropping systems have been regarded as the practical application of basic ecological principles such as diversity, competition and facilitation. In a recent PNAS paper, Li et al. (1) describe the novel finding that maize exudates promote faba bean nodulation and nitrogen fixation by upregulating genes involved in (iso)flavonoids synthesis (chalcone-flavanone isomerase) within faba bean, resulting in production of more genistein, a legume-to-rhizobia signal during establishment of the faba bean N2-fixing symbiosis. Although we salute the authors methodological efforts, there is another mechanism that could be responsible for the effect of corn root exudates on faba been nitrogen fixation observed in this article (1). The authors may misunderstand their data and the signalling role of maize exudates, thus got a defective model for the root interactions between faba bean and maize.

plant biology↗

bioRxiv2016

Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction

The binding and contribution of transcription factors (TF) to cell specific gene expression is often deduced from open-chromatin measurements to avoid costly TF ChIP-seq assays. Thus, it is important to develop computational methods for accurate TF binding prediction in open-chromatin regions (OCRs). Here, we report a novel segmentation-based method, TEPIC, to predict TF binding by combining sets of OCRs with position weight matrices. TEPIC can be applied to various open-chromatin data, e.g. DNaseI-seq and NOMe-seq. Additionally, Histone-Marks (HMs) can be used to identify candidate TF binding sites. TEPIC computes TF affinities and uses open-chromatin/HM signal intensity as quantitative measures of TF binding strength. Using machine learning, we find low affinity binding sites to improve our ability to explain gene expression variability compared to the standard presence/absence classification of binding sites. Further, we show that both footprints and peaks capture essential TF binding events and lead to a good prediction performance. In our application, gene-based scores computed by TEPIC with one open-chromatin assay nearly reach the quality of several TF ChIP-seq datasets. Finally, these scores correctly predict known transcriptional regulators as illustrated by the application to novel DNaseI-seq and NOMe-seq data for primary human hepatocytes and CD4+ T-cells, respectively.

bioinformatics↗