Automated quantification of vacuole fusion and lipophagy in Saccharomyces cerevisiae from fluorescence and cryo-soft X-ray microscopy data using deep learning

Remodeling of yeast vacuole membrane lipidomes from the log (one phase) to stationary stage (two phases)

(2023) John Reinhard et al.   BIOPHYSICAL JOURNAL

Fatty Acyl Coenzyme A Synthetase Fat1p Regulates Vacuolar Structure and Stationary-Phase Lipophagy in Saccharomyces cerevisiae

(2023) Fan Qiu et al.   Microbiology Spectrum

Iron Limitation Restores Autophagy and Increases Lifespan in the Yeast Model of Niemann–Pick Type C1

(2023) Telma S. Martins et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

A role for lipophagy in atherosclerosis

(2023) Thomas Laval et al.   Nature Reviews Cardiology

YeastMate: Neural network-assisted segmentation of mating and budding events in S. cerevisiae

(2022) David Bunk et al.   BIOINFORMATICS

Yeast cells actively tune their membranes to phase separate at temperatures that scale with growth temperatures

(2022) Chantelle L. Leveille et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Soft X-ray tomography to map and quantify organelle interactions at the mesoscale

(2022) Valentina Loconte et al.   STRUCTURE

Molecular and Cellular Bases of Lipodystrophy Syndromes

(2022) Jamila Zammouri et al.   Frontiers in Endocrinology

Phenomics approaches to understand genetic networks and gene function in yeast

(2022) Clarence Hue Lok Yeung et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Auto-segmentation and time-dependent systematic analysis of mesoscale cellular structure in β-cells during insulin secretion

(2022) Angdi Li et al.   PLoS One

Lipophagy pathways in yeast are controlled by their distinct modes of induction

(2022) Garrett Fairman et al.   YEAST

An intensity-based post-processing tool for 3D instance segmentation of organelles in soft X-ray tomograms

(2022) Angdi Li et al.   PLoS One

Defective iron homeostasis and hematological abnormalities in Niemann-Pick disease type C1

(2022) Oscar C W Chen et al.   Wellcome Open Research

Niemann Pick C2 protein enables cholesterol transfer from endo-lysosomes to the plasma membrane for efflux by shedding of extracellular vesicles

(2021) Alice Dupont Juhl et al.   CHEMISTRY AND PHYSICS OF LIPIDS

Lipid droplets and autophagy—links and regulations from yeast to humans

(2021) Jana Schepers et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

The ménage à trois of autophagy, lipid droplets and liver disease

(2021) Yasmina Filali-Mouncef et al.   Autophagy

Sample preparation strategies for efficient correlation of 3D SIM and soft X-ray tomography data at cryogenic temperatures

(2021) Chidinma A. Okolo et al.   Nature Protocols

Quantitative imaging of membrane contact sites for sterol transfer between endo-lysosomes and mitochondria in living cells

(2021) Alice Dupont Juhl et al.   Scientific Reports

Identification of novel lipid droplet factors that regulate autophagy and cholesterol efflux in macrophage foam cells

(2021) S. Robichaud et al.   ATHEROSCLEROSIS

CellProfiler Analyst 3.0: accessible data exploration and machine learning for image analysis

(2021) David R Stirling et al.   BIOINFORMATICS

Lipid droplets in the nervous system

(2021) Isha Ralhan et al.   JOURNAL OF CELL BIOLOGY

Loss odyssey in medical image segmentation

(2021) Jun Ma et al.   MEDICAL IMAGE ANALYSIS

Quantitative live-cell PALM reveals nanoscopic Faa4 redistributions and dynamics on lipid droplets during metabolic transitions of yeast

(2021) Santosh Adhikari et al.   MOLECULAR BIOLOGY OF THE CELL

Cryptococcus extracellular vesicles properties and their use as vaccine platforms

(2021) Juliana Rizzo et al.   Journal of Extracellular Vesicles

Roles for L o microdomains and ESCRT in ER stress-induced lipid droplet microautophagy in budding yeast

(2021) Pin-Chao Liao et al.   MOLECULAR BIOLOGY OF THE CELL

DeepImageJ: A user-friendly environment to run deep learning models in ImageJ

(2021) Estibaliz Gómez-de-Mariscal et al.   NATURE METHODS

Iron chelation by deferiprone does not rescue the Niemann-Pick Disease Type C1 mouse model

(2020) Ya Hui Hung et al.   BIOMETALS

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

Lipid Droplets in Neurodegenerative Disorders

(2020) Brandon C. Farmer et al.   Frontiers in Neuroscience

NPC1-mTORC1 Signaling Couples Cholesterol Sensing to Organelle Homeostasis and Is a Targetable Pathway in Niemann-Pick Type C

(2020) Oliver B. Davis et al.   DEVELOPMENTAL CELL

Cellpose: a generalist algorithm for cellular segmentation

(2020) Carsen Stringer et al.   NATURE METHODS

A Novel Protocol for the Isolation of Fungal Extracellular Vesicles Reveals the Participation of a Putative Scramblase in Polysaccharide Export and Capsule Construction in Cryptococcus gattii

(2019) Flavia C. G. Reis et al.   mSphere

NPC intracellular cholesterol transporter 1 (NPC1)-mediated cholesterol export from lysosomes

(2019) Suzanne R. Pfeffer   JOURNAL OF BIOLOGICAL CHEMISTRY

DeepPhagy: a deep learning framework for quantitatively measuring autophagy activity in Saccharomyces cerevisiae

(2019) Ying Zhang et al.   Autophagy

Structural Insight into Eukaryotic Sterol Transport through Niemann-Pick Type C Proteins

(2019) Mikael B.L. Winkler et al.   CELL

An evaluation of machine-learning for predicting phenotype: studies in yeast, rice, and wheat

(2019) Nastasiya F. Grinberg et al.   MACHINE LEARNING

Single organelle dynamics linked to 3D structure by correlative live-cell imaging and 3D electron microscopy

(2018) Job Fermie et al.   TRAFFIC

Saccharomyces cerevisiae adapted to grow in the presence of low-dose rapamycin exhibit altered amino acid metabolism

(2018) Duygu Dikicioglu et al.   Cell Communication and Signaling

AnatomyNet: Deep learning for fast and fully automated whole-volume segmentation of head and neck anatomy

(2018) Wentao Zhu et al.   MEDICAL PHYSICS

U-Net: deep learning for cell counting, detection, and morphometry

(2018) Thorsten Falk et al.   NATURE METHODS

The Participation of Regulatory Lipids in Vacuole Homotypic Fusion

(2018) Matthew L. Starr et al.   TRENDS IN BIOCHEMICAL SCIENCES

Regulation of lipid droplets by metabolically controlled Ldo isoforms

(2017) Vitor Teixeira et al.   JOURNAL OF CELL BIOLOGY

Automated analysis of high‐content microscopy data with deep learning

(2017) Oren Z Kraus et al.   Molecular Systems Biology

Lysosomal cholesterol activates mTORC1 via an SLC38A9–Niemann-Pick C1 signaling complex

(2017) Brian M. Castellano et al.   SCIENCE

Niemann-Pick type C proteins promote microautophagy by expanding raft-like membrane domains in the yeast vacuole

(2017) Takuma Tsuji et al.   eLife

AMPK and vacuole-associated Atg14p orchestrate μ-lipophagy for energy production and long-term survival under glucose starvation

(2017) Arnold Y Seo et al.   eLife

MorphoLibJ: integrated library and plugins for mathematical morphology with ImageJ

(2016) David Legland et al.   BIOINFORMATICS

A defect of the vacuolar putative lipase Atg15 accelerates degradation of lipid droplets through lipolysis

(2015) Yuichiro Maeda et al.   Autophagy

Lipid droplets and their component triglycerides and steryl esters regulate autophagosome biogenesis

(2015) T. Shpilka et al.   EMBO JOURNAL

Tomo3D 2.0 – Exploitation of Advanced Vector eXtensions (AVX) for 3D reconstruction

(2015) Jose-Ignacio Agulleiro et al.   JOURNAL OF STRUCTURAL BIOLOGY

The vacuole vs. the lysosome

(2014) Daniel J Klionsky et al.   Autophagy

A sterol-enriched vacuolar microdomain mediates stationary phase lipophagy in budding yeast

(2014) Chao-Wen Wang et al.   JOURNAL OF CELL BIOLOGY

A marker-free automatic alignment method based on scale-invariant features

(2014) Renmin Han et al.   JOURNAL OF STRUCTURAL BIOLOGY

Direct imaging reveals stable, micrometer-scale lipid domains that segregate proteins in live cells

(2013) Alexandre Toulmay et al.   JOURNAL OF CELL BIOLOGY

Lipid droplet autophagy in the yeast Saccharomyces cerevisiae

(2013) Tim van Zutphen et al.   MOLECULAR BIOLOGY OF THE CELL

Sphingolipid signalling mediates mitochondrial dysfunctions and reduced chronological lifespan in the yeast model of Niemann-Pick type C1

(2013) Rita Vilaça et al.   MOLECULAR MICROBIOLOGY

An Algorithm to Automate Yeast Segmentation and Tracking

(2013) Andreas Doncic et al.   PLoS One

Counting molecules in single organelles with superresolution microscopy allows tracking of the endosome maturation trajectory

(2013) E. M. Puchner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Imaging endosomes and autophagosomes in whole mammalian cells using correlative cryo-fluorescence and cryo-soft X-ray microscopy (cryo-CLXM)

(2013) Elizabeth M.H. Duke et al.   ULTRAMICROSCOPY

Cryo X-ray microscope with flat sample geometry for correlative fluorescence and nanoscale tomographic imaging

(2012) Gerd Schneider et al.   JOURNAL OF STRUCTURAL BIOLOGY

Cell-free reconstitution of vacuole membrane fragmentation reveals regulation of vacuole size and number by TORC1

(2012) Lydie Michaillat et al.   MOLECULAR BIOLOGY OF THE CELL

Identification of Surface Residues on Niemann-Pick C2 Essential for Hydrophobic Handoff of Cholesterol to NPC1 in Lysosomes

(2010) Michael L. Wang et al.   Cell Metabolism

Metabolic Response to Iron Deficiency in Saccharomyces cerevisiae

(2010) Minoo Shakoury-Elizeh et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Three-dimensional cellular ultrastructure resolved by X-ray microscopy

(2010) Gerd Schneider et al.   NATURE METHODS

Characterization of Yeast Extracellular Vesicles: Evidence for the Participation of Different Pathways of Cellular Traffic in Vesicle Biogenesis

(2010) Débora L. Oliveira et al.   PLoS One

Cholesterol trafficking is required for mTOR activation in endothelial cells

(2010) J. Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantitative analysis of yeast internal architecture using soft X-ray tomography

(2010) Maho Uchida et al.   YEAST

Autophagy regulates lipid metabolism

(2009) Rajat Singh et al.   NATURE

Soft X-ray tomography of phenotypic switching and the cellular response to antifungal peptoids in Candida albicans

(2009) M. Uchida et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Soft X-ray tomography and cryogenic light microscopy: the cool combination in cellular imaging

(2009) Gerry McDermott et al.   TRENDS IN CELL BIOLOGY

The yeast lysosome-like vacuole: Endpoint and crossroads

(2008) Sheena Claire Li et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH