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Creators/Authors contains: "Zhu, Jie"

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  1. Abstract

    Transitioning from pluripotency to differentiated cell fates is fundamental to both embryonic development and adult tissue homeostasis. Improving our understanding of this transition would facilitate our ability to manipulate pluripotent cells into tissues for therapeutic use. Here, we show that membrane voltage (Vm) regulates the exit from pluripotency and the onset of germ layer differentiation in the embryo, a process that affects both gastrulation and left-right patterning. By examining candidate genes of congenital heart disease and heterotaxy, we identifyKCNH6, a member of the ether-a-go-go class of potassium channels that hyperpolarizes the Vmand thus limits the activation of voltage gated calcium channels, lowering intracellular calcium. In pluripotent embryonic cells, depletion ofkcnh6leads to membrane depolarization, elevation of intracellular calcium levels, and the maintenance of a pluripotent state at the expense of differentiation into ectodermal and myogenic lineages. Using high-resolution temporal transcriptome analysis, we identify the gene regulatory networks downstream of membrane depolarization and calcium signaling and discover that inhibition of the mTOR pathway transitions the pluripotent cell to a differentiated fate. By manipulating Vmusing a suite of tools, we establish a bioelectric pathway that regulates pluripotency in vertebrates, including human embryonic stem cells.

  2. Free, publicly-accessible full text available May 1, 2023
  3. Abstract

    Structured Illumination Microscopy enables live imaging with sub-diffraction resolution. Unfortunately, optical aberrations can lead to loss of resolution and artifacts in Structured Illumination Microscopy rendering the technique unusable in samples thicker than a single cell. Here we report on the combination of Adaptive Optics and Structured Illumination Microscopy enabling imaging with 150 nm lateral and 570 nm axial resolution at a depth of 80 µm throughCaenorhabditis elegans. We demonstrate that Adaptive Optics improves the three-dimensional resolution, especially along the axial direction, and reduces artifacts, successfully realizing 3D-Structured Illumination Microscopy in a variety of biological samples.

  4. Recently, metal–organic framework (MOF)-based polymeric substrates show promising performance in many engineering and technology fields. However, a commonly known drawback of MOF/polymer composites is MOF crystal encapsulation and reduced surface area. This work reports a facile and gentle strategy to produce self-supported MOF predominant hollow fiber mats. A wide range of hollow MOFs including MIL-53(Al)–NH 2 , Al-PMOF, and ZIF-8 are successfully fabricated by our synthetic method. The synthetic strategy combines atomic layer deposition (ALD) of metal oxides onto polymer fibers and subsequent selective removal of polymer components followed by conversion of remaining hollow metal oxides into freestanding MOF predominant hollow fiber structures. The hollow MOFs show boosted surface area, superb porosity, and excellent pore accessibility, and exhibit a significantly improved performance in CO 2 adsorption (3.30 mmol g −1 ), CO 2 /N 2 separation selectivity (24.9 and 21.2 for 15/85 and 50/50 CO 2 /N 2 mixtures), and catalytic removal of HCHO (complete oxidation of 150 ppm within 60 min).
  5. Abstract Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and complex datasets with long- and short-read sequences, created computationally from around 1,700 new and known genomes, as well as 600 new plasmids and viruses. Here we analyze 5,002 results by 76 program versions. Substantial improvements were seen in assembly, some due to long-read data. Related strains still were challenging for assembly and genome recovery through binning, as was assembly quality for the latter. Profilers markedly matured, with taxon profilers and binners excelling at higher bacterial ranks, but underperforming for viruses and Archaea. Clinical pathogen detection results revealed a need to improve reproducibility. Runtime and memory usage analyses identified efficient programs, including top performers with other metrics. The results identify challenges and guide researchers in selecting methods for analyses.
    Free, publicly-accessible full text available April 1, 2023