A5101547765- Microfluidic and Bio-sensing Technologies
- Microfluidic and Capillary Electrophoresis Applications
- Innovative Microfluidic and Catalytic Techniques Innovation
- Cancer Cells and Metastasis
- Genomics and Chromatin Dynamics
- Cell Image Analysis Techniques
- Plant Molecular Biology Research
- Advanced Sensor and Energy Harvesting Materials
- 3D Printing in Biomedical Research
- Electrospun Nanofibers in Biomedical Applications
- RNA Research and Splicing
- Nanofabrication and Lithography Techniques
- RNA modifications and cancer
- Biosensors and Analytical Detection
- Carbon Nanotubes in Composites
- Advanced biosensing and bioanalysis techniques
- Surface Modification and Superhydrophobicity
- Machine Learning in Bioinformatics
- CRISPR and Genetic Engineering
- Single-cell and spatial transcriptomics
- Electrowetting and Microfluidic Technologies
- Gene Regulatory Network Analysis
- Cancer Genomics and Diagnostics
- HIV Research and Treatment
- Molecular Biology Techniques and Applications
EMBL Australia
2022-2024
UNSW Sydney
2022-2024
University of Kentucky
2024
University of Zurich
2021-2024
University of Wisconsin–Madison
2011-2022
Wisconsin Institutes for Discovery
2012-2018
Madison Group (United States)
2017-2018
Norwich Research Park
2012-2017
John Innes Centre
2012-2017
Salus (United States)
2016
Gene silencing by Polycomb complexes is central to eukaryotic development. Cold-induced epigenetic repression of FLOWERING LOCUS C (FLC) in the plant Arabidopsis provides an opportunity study initiation and maintenance silencing. Here, we show that a subset repressive complex 2 factors nucleate small region within FLC, locally increasing H3K27me3 levels. This nucleation confers silenced state metastably inherited, with memory held local chromatin. Metastable then converted stable through...
Using various nanomanipulating instruments, solvated polymers are simultaneously formed into fibers, adhered to solid supports, and interconnected in real-time create suspended fiber bridges networks of specified geometries. Fibers from 50 nm 20 μm diameter have been drawn individually parallel using single tips tip arrays. The speed ease producing three-dimensional structures recommends the method for application custom fabrication prototype microfluidic microoptical devices.
The extraction and purification of nucleic acids from complex samples (e.g. blood, biopsied tissue, cultured cells, food) is an essential prerequisite for many applications in biology including genotyping, transcriptional analysis, systems biology, epigenetic virus/bacterial detection. In this report, we describe a new process acid that utilizes "pinned" aqueous/organic liquid interfaces microchannels to streamline the mechanism, replacing all washing steps with single traverse immiscible...
We study discrete-time quantum walks on the line and general undirected graphs with two interacting or noninteracting particles. introduce simple interaction schemes show that they both lead to a diverse range of probability distributions depend correlations relative phases between initial coin states investigate characteristics these time evolution entanglement particles from separable entangled states. also test capability two-particle distinguish nonisomorphic graphs. For strongly regular...
Genes targeted by Polycomb repressive complex 2 (PRC2) are regulated in cis chromatin modifications and also trans diffusible regulators such as transcription factors. Here, we introduce a mathematical model which directly antagonizes silencing, thereby linking these cis- trans-regulatory inputs to gene expression. The is parameterized recent experimental data showing that PRC2-mediated accumulate extremely slowly. generates self-perpetuating, bistable active repressed states persist through...
Inheritance of gene expression states is fundamental for cells to 'remember' past events, such as environmental or developmental cues. The conserved Polycomb Repressive Complex 2 (PRC2) maintains epigenetic repression many genes in animals and plants modifies chromatin at its targets. Histones modified by PRC2 can be inherited through cell division. However, it remains unclear whether this inheritance direct long-term memory individual (cis memory) instead if local are dictated the...
Abstract Highly multiplexed imaging holds enormous promise for understanding how spatial context shapes the activity of genome and its products at multiple length scales. Here, we introduce a deep learning framework called CAMPA (Conditional Autoencoder Multiplexed Pixel Analysis), which uses conditional variational autoencoder to learn representations molecular pixel profiles that are consistent across heterogeneous cell populations experimental perturbations. Clustering these pixel-level...
Abstract Purpose: There is a critical clinical need for new predictive and pharmacodynamic biomarkers that evaluate pathway activity in patients treated with targeted therapies. A microscale platform known as VERSA (versatile exclusion-based rare sample analysis) was developed to integrate readouts across protein, mRNA, DNA circulating tumor cells (CTC) comprehensive analysis of the androgen receptor (AR) signaling pathway. Experimental Design: Utilizing preparation principles, handheld chip...
We study the discrete-time quantum-walk-based search for a marked vertex on graph. By considering various structures in which not all vertices are equivalent, we investigate relationship between successful probability and position of vertex, particular, its centrality. find that maximum value does necessarily increase as becomes more central, an interesting frequency centrality vertex.
Isolation and characterization of a specific subset cells from large heterogeneous population is necessary for studying rare subpopulations cells. Existing methods require transfer or wash steps that risk causing loss the cell interest. Integrated reduce loss, making these especially useful reliable isolation populations. In this report, we demonstrate VerIFAST, device builds upon simplified workflow Immiscible Filtration Assisted by Surface Tension (IFAST) to integrate method cellular with...
Background Expression of programmed-death ligand 1 (PD-L1) in non-small cell lung cancer (NSCLC) is typically evaluated through invasive biopsies; however, recent advances the identification circulating tumor cells (CTCs) may be a less method to assay for these purposes. These liquid biopsies rely on accurate CTCs from diverse populations blood, where some share characteristics with normal blood cells. While many can excluded by their high expression CD45, neutrophils and other immature...
The micro-Wilhelmy method is a well-established of determining surface tension by measuring the force withdrawing tens microns to millimeters in diameter cylindrical wire or fiber from liquid. A comparison insertion retraction can also be used determine contact angle with fiber. Given limited availability atomic microscope (AFM) probes that have long constant tips, force−distance (F−D) curves using standard tapered tips been difficult relate tension. In this report, metal alloy nanowires...
Significance Lipopolysaccharides (LPSs) are unique glycolipids that characteristic components of outer membranes in Gram negative bacteria and play important roles pathogenesis. Many LPSs contain a long-chain polysaccharide (known as the O antigen) whose length can be an factor bacterial resistance to complement-mediated killing. While involved chain-length determination known many systems, underlying regulatory mechanism is not. Here we apply mathematical modeling approach integrates...
Abstract Arrayed CRISPR libraries extend the scope of gene-perturbation screens but require large numbers efficacious sgRNA-expressing vectors. Using a newly invented liquid-phase plasmid cloning methodology, we constructed genome-wide arrayed for human gene ablation (19,936 plasmids), activation, and epigenetic silencing (22,442 plasmids). At least 76% each preparation encoded an intact array 4 non-overlapping sgRNAs designed to tolerate most DNA polymorphisms. We achieved perturbation...
RNA polymerase II (Pol II) is the multi-protein complex responsible for transcribing all protein-coding messenger (mRNA). Most research on gene regulation focused mechanisms controlling which genes are transcribed when, or mechanics of transcription. How global Pol activity determined receives comparatively less attention. Here, we follow life a molecule from 'assembly complex' to nuclear import, enzymatic activity, and degradation. We focus how spends its time in nucleus, two-way...
Immunoassays are utilized for a wide variety of clinical and biomedical research applications. In typical immunoassays, analytes captured, labeled, quantified on single surface (e.g., the bottom well plate). order to minimize background, this type assay must be washed multiple times between each these steps ensure residual reagents unbound labeling antibody) removed from system. manuscript, immunoassay is fundamentally reconfigured, such that reagent confined its own no wash required. Using...
The path from gene (DNA) to product (RNA or protein) is the foundation of genotype giving rise phenotype. Comparison genomic analyses with paired transcriptomic studies (mRNA) critical evaluating pathogenic processes that give human disease. ability analyze both DNA and mRNA same sample not only important for biologic interrogation but also minimize variance (e.g., loss) unrelated biology. Existing methods RNA purification a single are typically time-consuming labor intensive require large...
Epigenetic maintenance of gene repression is essential for development. Polycomb complexes are central to this memory, but many aspects the underlying mechanism remain unclear. LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) binds Polycomb-deposited H3K27me3 and required target genes in Arabidopsis . Here we show that LHP1 RNA vitro through intrinsically disordered hinge region. By independently perturbing RNA-binding region (trimethylation histone H3 at Lys27) recognition, found both facilitate...
The purification of analytes is an important prerequisite for many analytical processes. Although automated infrastructure has dramatically increased throughput these processes, the upstream analyte lagged behind, partially due to complexity conventional isolation Here, we demonstrate operation arrays a new sample preparation technology--immiscible filtration assisted by surface tension (IFAST). IFAST uses position immiscible liquid barrier between biological and downstream buffer....