900+ Papers found (0.012 seconds)

Wu Y et al. (2021) Nature "Multiview confocal super-resolution microscopy."

[

Nature,

2021]

Confocal microscopy1 remains a major workhorse in biomedical optical microscopy owing to its reliability and flexibility in imaging various samples, but suffers from substantial point spread function anisotropy, diffraction-limited resolution, depth-dependent degradation in scattering samples and volumetric bleaching2. Here we address these problems, enhancing confocal microscopy performance from the sub-micrometre to millimetre spatial scale and the millisecond to hour temporal scale, improving both lateral and axial resolution more than twofold while simultaneously reducing phototoxicity. We achieve these gains using an integrated, four-pronged approach: (1) developing compact line scanners that enable sensitive, rapid, diffraction-limited imaging over large areas; (2) combining line-scanning with multiview imaging, developing reconstruction algorithms that improve resolution isotropy and recover signal otherwise lost to scattering; (3) adapting techniques from structured illumination microscopy, achieving super-resolution imaging in densely labelled, thick samples; (4) synergizing deep learning with these advances, further improving imaging speed, resolution and duration. We demonstrate these capabilities on more than 20 distinct fixed and live samples, including protein distributions in single cells; nuclei and developing neurons in Caenorhabditis elegans embryos, larvae and adults; myoblasts in imaginal disks of Drosophila wings; and mouse renal, oesophageal, cardiac and brain tissues.

Wu Y-C et al. (1993) International C. elegans Meeting "Analysis of the sur-1 gene in C.elegans."

Wu Y-C, Han M

[

International C. elegans Meeting,

1993]

Wu Y-C et al. (1997) International C. elegans Meeting "TUNELING FOR CORPSES IN C. ELEGANS"

Horvitz HR, Wu Y-C, Stanfield GM

[

International C. elegans Meeting,

1997]

The principal assay for cell death in C. elegans has been light microscopic observation using Nomarski optics of dying cells, which are readily distinguishable by their raised, refractile appearance. Some cell- death mutants affect the morphology or time of appearance of cell corpses as visualized by Nomarski optics, so it would be useful to have additional markers to follow the progression of the cell-death process. We have adapted the TUNEL (TdT-mediated dUTP Nick End Labeling) technique (1) for studies in C. elegans. TUNEL has been widely used to identify cell corpses in other organisms. TUNEL specifically labels DNA ends, which are more abundant in cell corpses as a consequence of DNA degradation. Thus, in C. elegans, TUNEL should provide both an additional marker for cell corpses and a tool for studying the control of DNA degradation during programmed cell death. We found that TUNEL stains only a small subset of the cell corpses visualized in wild-type embryos using Nomarski optics. However, nuc-1 embryos, which are defective in some aspects of DNA degradation (2,3,4), contain many persistent TUNEL-positive nuclei. Since ced-3, ced-4, and ced-9(gf) mutations significantly reduce TUNEL-staining in a nuc-1 background, the TUNEL-positive nuclei are likely to be those of cell corpses. We propose that DNA degradation is normally very rapid in dying cells, that only certain transient intermediates are TUNEL-reactive, and that mutations in nuc-1 may block DNA degradation from proceeding beyond the TUNEL-reactive stage(s). If so, DNA degradation may involve multiple steps, only some of which are mediated by nuc-1. We have begun to use the TUNEL technique to stain other cell-death mutants. We have found that some mutants with previously indistinguishable engulfment-defective phenotypes have distinct TUNEL-staining patterns. These results indicate that some steps in DNA degradation are dependent on engulfment gene function. (1) Gavrieli et al., J. Cell Biol. 119, 493, 1992 (2) Sulston, Philos. Trans. R. Soc. London 275, 287, 1976 (3) Hedgecock et al., Science 220, 1277, 1983 (4) Hevelone & Hartman, Biochem. Genetics 26, 447, 1988

Wu Y et al. (2005) Curr Alzheimer Res "Transgenic C. elegans as a model in Alzheimer's research."

Wu Y, Luo Y

[

Curr Alzheimer Res,

2005]

Alzheimer''''s disease (AD) has been associated with aggregation of beta-amyloid peptide (Abeta) and cell death in the brain. Using various models, such as the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster and the mouse Mus musculus, investigators have attempted to imitate the pathology process of AD for better understanding of the cellular mechanisms and for possible therapeutic intervention. Among many in vitro and in vivo models of AD, transgenic C. elegans expressing human Abeta has shown its own advantages. The transgenic C. elegans model have been used in studying AD due to its short life span, facility to maintain, ability to develop muscle-associated deposits reactive to amyloid-specific dyes and the concomitant progressive paralysis phenotype. Moreover, the transgenic C. elegans exhibits increased levels of reactive oxygen species (ROS) and protein carbonyls, similar to those observed in AD patients, supporting the current theory on Abeta-induced oxidative stress and subsequent neurodegeneration in AD. DNA microarray assays of the worm demonstrated several stress-related genes being upregulated, particularly two genes homologous to human alphaB-crystallin and tumor necrosis factor-related protein, which were also upregulated in postmortem AD brain. Studies in our laboratory along with others suggest that the transgenic C. elegans model is a suitable in vivo model to relate Abeta-expression with its toxicity, which may underlie AD pathology. It may also be used as a tool for pharmacological evaluation of novel therapeutic agents.

Wu Y et al. (2017) Curr Top Dev Biol "Regulation of Cell Polarity by PAR-1/MARK Kinase."

Wu Y, Griffin EE

[

Curr Top Dev Biol,

2017]

PAR-1/MARK kinases are conserved serine/threonine kinases that are essential regulators of cell polarity. PAR-1/MARK kinases localize and function in opposition to the anterior PAR proteins to control the asymmetric distribution of factors in a wide variety polarized cells. In this review, we discuss the mechanisms that control the localization and activity of PAR-1/MARK kinases, including their antagonistic interactions with the anterior PAR proteins. We focus on the role PAR-1 plays in the asymmetric division of the Caenorhabditis elegans zygote, in the establishment of the anterior/posterior axis in the Drosophila oocyte and in the control of microtubule dynamics in mammalian neurons. In addition to conserved aspects of PAR-1 biology, we highlight the unique ways in which PAR-1 acts in these distinct cell types to orchestrate their polarization. Finally, we review the connections between disruptions in PAR-1/MARK function and Alzheimer's disease and cancer.

Wu Y et al. (2024) MicroPubl Biol "RAL-1 signaling regulates lipid composition in C. elegans."

Mutlu AS, Wang M, Lee M, Wu Y, Reiner DJ

[

MicroPubl Biol,

2024]

Signaling by the Ral small GTPase is poorly understood in vivo . Caenorhabditis elegans animals with constitutively activated RAL-1 or deficient for the inhibitory RalGAP, HGAP-1 /2, display pale intestines. Staining with Oil Red O detected decreased intestinal lipids in the hgap-1 deletion mutant relative to the wild type. Constitutively activated RAL-1 decreased lipid detected by stimulated Raman scattering (SRS) microscopy, a label-free method of detecting lipid by laser excitation and detection. A signaling-deficient missense mutant for RAL-1 also displayed reduced lipid staining via SRS. We conclude that RAL-1 signaling regulates lipid homeostasis, biosynthesis or storage in live animals.

Wu Y-C et al. (2000) West Coast Worm Meeting "Rac-like GTPases and cell migration"

Wu Y-C, Cheng T-W, Weng N-Y, Cheng L-C

[

West Coast Worm Meeting,

2000]

Cytoskeletal rearrangement and cell polarization are important for fundamental cellular processes, such as cell migration and the phagocytosis of apoptotic cells. We are interested in how migration cues and apoptotic signals are interpreted by the receiving cells and subsequently affect their cytoskeletal rearrangement during cell migration and cell-corpse-phagocytosis in Caenorhabditis elegans. At least two C. elegans Rac-like GTPases have been shown to be important for cell migration. MIG-2 is necessary for the migration of Q cells, Q cell descendents and coelomocytes (1). CED-10 is important for the migration of distal tip cells as well as the engulfment of apoptotic cells (2). To test if these two GTPases may function redundantly in the migration of other cells, we have constructed ced-10;mig-2 double mutants and are currently analyzing the mutant phenotype. It has been proposed that ced-10 may function downstream of ced-2 and ced-5 during cell-corpse-engulfment (2). We have also constructed ced-2; mig-2 and ced-5; mig-2 double mutants. Results will be presented at the meeting. Zipkin et al., Cell, 90, 883-894 (1997) Reddien and Horvitz, Nature Cell Biology, 2, 131-136 (2000)

Wu Y et al. (2014) EMBO Rep "PI3P phosphatase activity is required for autophagosome maturation and autolysosome formation."

Zhao H, Wu Y, Yoshina S, Wang X, Cheng S, Mitani S, Zou W, Zhang H

[

EMBO Rep,

2014]

Autophagosome formation is promoted by the PI3 kinase complex and negatively regulated by myotubularin phosphatases, indicating that regulation of local phosphatidylinositol 3-phosphate (PtdIns3P) levels is important for this early phase of autophagy. Here, we show that the Caenorhabditis elegans myotubularin phosphatase MTM-3 catalyzes PtdIns3P turnover late in autophagy. MTM-3 acts downstream of the ATG-2/EPG-6 complex and upstream of EPG-5 to promote autophagosome maturation into autolysosomes. MTM-3 is recruited to autophagosomes by PtdIns3P, and loss of MTM-3 causes increased autophagic association of ATG-18 in a PtdIns3P-dependent manner. Our data reveal critical roles of PtdIns3P turnover in autophagosome maturation and/or autolysosome formation.

Wu Y-C et al. (1993) Worm Breeder's Gazette "Functional Homology Between C. elegans and Mammalian MAP Kinases"

Han M, Wu Y-C

[

Worm Breeder's Gazette,

1993]

At the 1993 C. elegans meeting, we reported our genetic and molecular analysis of the C. elegans sur-1 /MAP kinase gene. The sur-1 gene (suppressor of ras mutation) was identified by a mutation that completely suppresses the Muv phenotype of let-60 (nlO46gf). Our analyses of the gene suggest that it is likely to act downstream of let-60 ras in the signaling pathway. The sur-1 gene was cloned by genetic and RFLP mapping and DNA-mediated transformation. The predicted open reading frame of the cDNA was translated into a protein of 376 amino acids. Comparison of the protein sequence to sequences in GenBank revealed a striking amino acid sequence similarity to the MAP kinase (Mitogen activated protein kinase) family of serine/threonine protein kinases. The sur-1 gene product is about 81% identical in amino acid sequence to mammalian ERK2 kinases (Extracellular signal-Regulated Kinase 2, also known as p42 MAP kinases) in a 339 amino-acid region (rat ERK2 has 358 amino acids). Mark Lackner in Stuart Kim's lab has also cloned the same MAP kinase gene by PCR and has shown the gene rescues a similar let-60 (gf)suppressor mutation isolated and studied by Kerry Kornfeld in Bob Horvitz's lab (reported in the 1993 meeting and personal communications). We performed a functional homology assay by introducing a rat ERK2 gene (essentially identical to human ERK2 )into C. elegans to see if it could complement the sur-1 mutation. A cDNA clone of the rat ERK2 gene (Boulton et al. 1991) was fused to the sur-1 regulatory region at the beginning of the predicted start codon. In addition, an unc-54 3' polyadenylation signal sequence (gift from A. Fire) was added at the 3' end of the ERK2 cDNA sequence. The fusion gene construct was then injected into a strain of genotype sur-1 (kul);let-60 (nlO46).The transgenic animals showed a highly penetrant Muv phenotype (>90%), indicating that the rat ERK2 gene can functionally complement sur-1 in C. elegans. The mammalian MAP kinase appears to be able to interact with factors acting upstream and downstream of the sur-1 gene product. The structural and functional homology between C. elegans sur-1 and mammalian ERK2 provide us with further evidence that the ras-mediated signal transduction pathways are extremely conserved between worm and human.

Wu Y et al. (2014) Cell "Multilayered genetic and omics dissection of mitochondrial activity in a mouse reference population."

Kutalik Z, Wolski W, Williams EG, Auwerx J, Aebersold R, Dubuis S, Zamboni N, Argmann CA, Faridi P, Houten SM, Jovaisaite V, Wu Y, Mottis A

[

Cell,

2014]

The manner by which genotype and environment affect complex phenotypes is one of the fundamental questions in biology. In this study, we quantified the transcriptome--a subset of the metabolome--and, using targeted proteomics, quantified a subset of the liver proteome from 40 strains of the BXD mouse genetic reference population on two diverse diets. We discovered dozens of transcript, protein, and metabolite QTLs, several of which linked to metabolic phenotypes. Most prominently, Dhtkd1 was identified as a primary regulator of 2-aminoadipate, explaining variance in fasted glucose and diabetes status in both mice and humans. These integrated molecular profiles also allowed further characterization of complex pathways, particularly the mitochondrial unfolded protein response (UPR(mt)). UPR(mt) shows strikingly variant responses at the transcript and protein level that are remarkably conserved among C. elegans, mice, and humans. Overall, these examples demonstrate the value of an integrated multilayered omics approach to characterize complex metabolic phenotypes.

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