A5075077010- Advanced X-ray Imaging Techniques
- Advanced Electron Microscopy Techniques and Applications
- Medical Imaging Techniques and Applications
- Advanced MRI Techniques and Applications
- Advanced X-ray and CT Imaging
- Cytomegalovirus and herpesvirus research
- Pickering emulsions and particle stabilization
- Herpesvirus Infections and Treatments
- Material Properties and Processing
- Advanced Fluorescence Microscopy Techniques
- Robotic Path Planning Algorithms
- Cell Image Analysis Techniques
- X-ray Spectroscopy and Fluorescence Analysis
- Robotics and Sensor-Based Localization
- Radiomics and Machine Learning in Medical Imaging
- Microbial Metabolic Engineering and Bioproduction
- Microbial Community Ecology and Physiology
- Pancreatic function and diabetes
- Enzyme Structure and Function
- interferon and immune responses
- RNA and protein synthesis mechanisms
- Advanced Cellulose Research Studies
- Advanced Neuroimaging Techniques and Applications
- Marine and coastal ecosystems
- Industrial Vision Systems and Defect Detection
University of California, San Francisco
2016-2024
Lawrence Berkeley National Laboratory
2017-2024
University of Jyväskylä
2012-2024
Advanced Light Source
2022-2023
Linköping University
1997
Swedish Defence Research Agency
1993
Symbiotic interactions were key to the evolution of chloroplast and mitochondria organelles, which mediate carbon energy metabolism in eukaryotes. Biological nitrogen fixation, reduction abundant atmospheric gas (N 2 ) biologically available ammonia, is a metabolic process performed exclusively by prokaryotes. Candidatus Atelocyanobacterium thalassa, or UCYN-A, metabolically streamlined N -fixing cyanobacterium previously reported be an endosymbiont marine unicellular alga. Here we show that...
Inter-organelle interactions are a vital part of normal cellular function; however, these have proven difficult to quantify due the range scales encountered in cell biology and throughput limitations traditional imaging approaches. Here, we demonstrate that soft X-ray tomography (SXT) can be used rapidly map ultrastructural reorganization inter-organelle intact cells. SXT takes advantage naturally occurring, differential absorption carbon-rich compounds each organelle. Specifically, use...
The protocol describes step-by-step sample preparation, data acquisition, and segmentation of cellular organelles with soft X-ray tomography. It is designed for microscopes built to perform full-rotation acquisition on specimens in cylindrical holders, such as the XM-2 microscope at Advanced Light Source, LBNL; however, it might be generalized similar holder designs both synchrotron table-top microscopes. For complete details use execution this profile, please refer Loconte et al. (2021).
Abstract Bacterial nucleoid remodeling dependent on conserved histone-like protein, HU is one of the determining factors in global gene regulation. By imaging near-native, unlabeled E. coli cells by soft X-ray tomography, we show that remodels nucleoids promoting formation a dense condensed core surrounded less isolated domains. Nucleoid during cell growth and environmental adaptation correlate with pH ionic strength controlled molecular switch regulated HUαα intermolecular DNA bundling....
Subcellular maps of β cells reveal the coordinated reorganization organelles during insulin secretion.
High-resolution and rapid imaging of host cell ultrastructure can generate insights toward viral disease mechanism, for example a severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. Here, we employ full-rotation soft X-ray tomography (SXT) to examine organelle remodeling induced by SARS-CoV-2 at the whole-cell level with high spatial resolution throughput. Most current SXT systems suffer from restricted field view due use flat sample supports artifacts missing data. In...
Maximizing the production of heterologous biomolecules is a complex problem that can be addressed with systems-level understanding cellular metabolism and regulation. Specifically, growth-coupling approaches increase product titers yields also enhance rates. However, implementing these methods for non-canonical carbon streams challenging due to gaps in metabolic models. Over four design-build-test-learn cycles, we rewire Pseudomonas putida KT2440 growth-coupled indigoidine from...
Positively charged repeat peptides are emerging as key players in neurodegenerative diseases. These can perturb diverse cellular pathways but a unifying framework for how such promiscuous toxicity arises has remained elusive. We used mass-spectrometry-based proteomics to define the protein targets of these neurotoxic and found that they all share similar sequence features drive their aberrant condensation with positively peptides. trained machine learning algorithm detect unexpectedly...
Positively charged repeat peptides are emerging as key players in neurodegenerative diseases. These can perturb diverse cellular pathways but a unifying framework for how such promiscuous toxicity arises has remained elusive. We used mass-spectrometry-based proteomics to define the protein targets of these neurotoxic and found that they all share similar sequence features drive their aberrant condensation with peptides. trained machine learning algorithm detect unexpectedly discovered this...
Viruses target mitochondria to promote their replication, and infection-induced stress during the progression of infection leads regulation antiviral defenses mitochondrial metabolism which are opposed by counteracting viral factors. The precise structural functional changes that underlie how react remain largely unclear. Here we show extensive transcriptional remodeling protein-encoding host genes involved in respiratory chain, apoptosis, organization as herpes simplex virus type 1 lytic...
The diversity of living cells, in both size and internal complexity, calls for imaging methods with adaptable spatial resolution. Soft x-ray tomography (SXT) is a three-dimensional technique ideally suited to visualizing quantifying the organization single cells varying sizes near-native state. achievable resolution soft microscope largely determined by objective lens, but switching between objectives extremely time-consuming typically undertaken only during maintenance procedures. Since...
Models of insulin secretory vesicles from pancreatic beta cells have been created using the cellPACK suite tools to research, curate, construct and visualise current state knowledge. The model integrates experimental information proteomics, structural biology, cryoelectron microscopy X-ray tomography, is used generate models mature immature vesicles. A new method was developed a confidence score that reconciles inconsistencies between three available proteomes expert annotations cellular...
Soft X‐ray tomography offers rapid imaging of whole, single cells with a few tens nanometers spatial resolution without fixation or labeling. Herein, this technique is limited to specimens about 10 μm thick, such that applications soft large human multicellular are not possible. A theoretical and experimental framework for enables extension volumes 18 μm‐thick developed. This approach, based on long depth field half‐acquisition tomography, easily applicable microscopes equipped full‐rotation...
During lytic herpes simplex virus 1 (HSV-1) infection, the expansion of viral replication compartments leads to an enrichment host chromatin in peripheral nucleoplasm. We have shown previously that HSV-1 infection induces formation channels through compacted chromatin. Here, we used three-dimensional confocal and microscopy, soft X-ray tomography, electron random walk simulations analyze kinetics redistribution capsid localization relative their egress site at nuclear envelope. Our data...
Abstract Mitochondria are dynamic organelles that change morphology to adapt cellular energetic demands under both physiological and stress conditions. Cardiomyopathies neuronal disorders associated with structure-related dysfunction in mitochondria, but three-dimensional characterizations of the still lacking. In this study, we combined high-resolution imaging 3D electron density information provided by cryo-soft X-ray tomography characterize mitochondria cristae isolated from murine. Using...
Upon infection, viruses hijack the cell machinery and remodel host structures to utilize them for viral proliferation. Since are about a thousand times smaller than their cells, imaging virus-host interactions at high spatial resolution is like looking needle in haystack. Scouting gross cellular changes with fluorescent microscopy only possible well-established viruses, where tagging developed. Soft X-ray tomography (SXT) offers 3D of entire cells without need chemical fixation or labeling....
Summary Recent developments in making fibre materials using the foam‐forming technology have raised a need to characterize porous structure at low material density. In order find an effective choice among all structure‐characterization methods, both two‐dimensional and three‐dimensional techniques were used explore of foam‐formed samples made with two different types cellulose fibre. These included X‐ray microtomography, scanning electron microscopy, light direct surface imaging CCD camera...
During starvation in the yeast Saccharomyces cerevisiae vacuolar vesicles fuse and lipid droplets (LDs) can become internalized into vacuole an autophagic process named lipophagy. There is a lack of tools to quantitatively assess starvation-induced fusion lipophagy intact cells with high resolution throughput. Here, we combine soft X-ray tomography (SXT) fluorescence microscopy use deep-learning computational approach visualize quantify these processes yeast. We focus on homologs mammalian...