In vivo biochemistry: quantifying ion and metabolite levels in individual cells or cultures of yeast

2011 ◽  
Vol 438 (1) ◽  
pp. 1-10 ◽  
Author(s):  
Clara Bermejo ◽  
Jennifer C. Ewald ◽  
Viviane Lanquar ◽  
Alexander M. Jones ◽  
Wolf B. Frommer
Keyword(s):  
Spatial Resolution ◽  
Time Resolution ◽  
Subcellular Distribution ◽  
Recent Progress ◽  
Yeast Cells ◽  
Fluorescent Indicators ◽  
Cellular Processes ◽  
The Past ◽  
Temporal And Spatial

Over the past decade, we have learned that cellular processes, including signalling and metabolism, are highly compartmentalized, and that relevant changes in metabolic state can occur at sub-second timescales. Moreover, we have learned that individual cells in populations, or as part of a tissue, exist in different states. If we want to understand metabolic processes and signalling better, it will be necessary to measure biochemical and biophysical responses of individual cells with high temporal and spatial resolution. Fluorescence imaging has revolutionized all aspects of biology since it has the potential to provide information on the cellular and subcellular distribution of ions and metabolites with sub-second time resolution. In the present review we summarize recent progress in quantifying ions and metabolites in populations of yeast cells as well as in individual yeast cells with the help of quantitative fluorescent indicators, namely FRET metabolite sensors. We discuss the opportunities and potential pitfalls and the controls that help preclude misinterpretation.

scholarly journals Recent advances in understanding circular RNAs

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 655 ◽  
Author(s):  
Constanze Ebermann ◽  
Theodor Schnarr ◽  
Sabine Müller
Keyword(s):  
Recent Progress ◽  
Circular Rnas ◽  
Ongoing Research ◽  
Model Studies ◽  
Cellular Processes ◽  
The Past ◽  
Recent Advances ◽  
Experimental Protocols

Exonic circular RNAs (circRNAs) have been discovered in all kingdoms of life. In many cases, the details of circRNA function and their involvement in cellular processes and diseases are not yet fully understood. However, the past few years have seen significant developments in bioinformatics and in experimental protocols that advance the ongoing research in this still-emerging field. Sophisticated methods for circRNA generation in vitro and in vivo have been developed, allowing model studies into circRNA function and application. We here review the ongoing circRNA research, giving special attention to recent progress in the field.

scholarly journals Sensitivity of ensemble Lagrangian reconstructions to assimilated wind time step resolution

2009 ◽  
Vol 9 (2) ◽  
pp. 8619-8633
Author(s):  
I. Pisso ◽  
V. Marécal ◽  
B. Legras ◽  
G. Berthet
Keyword(s):  
High Resolution ◽  
Spatial Resolution ◽  
Time Resolution ◽  
Wind Fields ◽  
Time Step ◽  
Coarse Resolution ◽  
Temporal And Spatial ◽  
Atmospheric Tracers

Abstract. The aim of this study is to define the optimal temporal and spatial resolution required for accurate offline diffusive Lagrangian reconstructions of high resolution in-situ tracers measurements based on meteorological wind fields and on coarse resolution 3-D tracer distributions. Increasing the time resolution of the advecting winds from three to one hour intervals has a modest impact on diffusive reconstructions in the case studied. This result is discussed in terms of the effect on the geometry of transported clouds of points in order to set out a method to assess the effect of meteorological flow on the transport of atmospheric tracers.

X-Ray Emission Associated with Filament Activity

1979 ◽  
Vol 44 ◽  
pp. 269-271 ◽  
Author(s):  
L.W. Acton ◽  
J.M. Mosher
Keyword(s):  
Spatial Resolution ◽  
Time Resolution ◽  
Active Regions ◽  
Spatial Relationships ◽  
Solar Plasma ◽  
X Ray ◽  
Small X ◽  
Temporal And Spatial

The purpose of this research is to investigate the temporal and spatial relationships of activated filaments, soft X-ray production, and Ha flares. The X-ray data are from the Lockheed Mapping X-Ray Heliometer (MXRH) on 0S0-8 (Wolfson et al., 1975, 1977). This instrument has been operating continuously since July 1975. It responds to radiation from solar plasma above about 2 × 106K, provides a time resolution of 20 sec, a spatial resolution of 2-3 arc min and has a basic sensitivity roughly equivalent to the 1-8 Å full disc monitors of, e.g., the SOLRAD and SMS/GOES satellites (threshold ≈ 2 × 10-9W/m2). However, because of its spatial resolution the MXRH permits study of small X-ray events in individual active regions even when the integrated solar X-ray emission is high.

scholarly journals Push–Pull Perfusion Sampling with Segmented Flow for High Temporal and Spatial Resolution in Vivo Chemical Monitoring

2011 ◽  
Vol 83 (13) ◽  
pp. 5207-5213 ◽  
Author(s):  
Thomas R. Slaney ◽  
Jing Nie ◽  
Neil D. Hershey ◽  
Prasanna K. Thwar ◽  
Jennifer Linderman ◽  
...  
Keyword(s):  
Spatial Resolution ◽  
Segmented Flow ◽  
Chemical Monitoring ◽  
Temporal And Spatial

scholarly journals Dietary, Metabolic, and Potentially Environmental Modulation of the Lysine Acetylation Machinery

2010 ◽  
Vol 2010 ◽  
pp. 1-14 ◽  
Author(s):  
Go-Woon Kim ◽  
Goran Gocevski ◽  
Chao-Jung Wu ◽  
Xiang-Jiao Yang
Keyword(s):  
Expression Patterns ◽  
Chromatin Dynamics ◽  
Cellular Processes ◽  
The Past ◽  
Pathological Conditions ◽  
Good State ◽  
Therapeutic Development ◽  
Dietary Components ◽  
External Stimuli

Healthy lifestyles and environment produce a good state of health. A number of scientific studies support the notion that external stimuli regulate an individual's epigenomic profile. Epigenetic changes play a key role in defining gene expression patterns under both normal and pathological conditions. As a major posttranslational modification, lysine (K) acetylation has received much attention, owing largely to its significant effects on chromatin dynamics and other cellular processes across species. Lysine acetyltransferases and deacetylases, two opposing families of enzymes governing K-acetylation, have been intimately linked to cancer and other diseases. These enzymes have been pursued by vigorous efforts for therapeutic development in the past 15 years or so. Interestingly, certain dietary components have been found to modulate acetylation levelsin vivo. Here we review dietary, metabolic, and environmental modulators of the K-acetylation machinery and discuss how they may be of potential value in the context of disease prevention.

Spiers Memorial Lecture : Surface-enhanced Raman spectroscopy: from single particle/molecule spectroscopy to ångstrom-scale spatial resolution and femtosecond time resolution

2017 ◽  
Vol 205 ◽  
pp. 9-30 ◽  
Author(s):  
Anne-Isabelle Henry ◽  
Tyler W. Ueltschi ◽  
Michael O. McAnally ◽  
Richard P. Van Duyne
Keyword(s):  
Raman Spectroscopy ◽  
Spatial Resolution ◽  
Single Molecule ◽  
Time Resolution ◽  
Glucose Sensor ◽  
Surface Enhanced Raman Spectroscopy ◽  
Memorial Lecture ◽  
Surface Enhanced ◽  
Surface Enhanced Raman

Four decades on, surface-enhanced Raman spectroscopy (SERS) continues to be a vibrant field of research that is growing (approximately) exponentially in scope and applicability while pushing at the ultimate limits of sensitivity, spatial resolution, and time resolution. This introductory paper discusses some aspects related to all four of the themes for this Faraday Discussion. First, the wavelength-scanned SERS excitation spectroscopy (WS-SERES) of single nanosphere oligomers (viz., dimers, trimers, etc.), the distance dependence of SERS, the magnitude of the chemical enhancement mechanism, and the progress toward developing surface-enhanced femtosecond stimulated Raman spectroscopy (SE-FSRS) are discussed. Second, our efforts to develop a continuous, minimally invasive, in vivo glucose sensor based on SERS are highlighted. Third, some aspects of our recent work in single molecule SERS and the translation of that effort to ångstrom-scale spatial resolution in ultrahigh vacuum tip-enhanced Raman spectroscopy (UHV-TERS) and single molecule electrochemistry using electrochemical (EC)-TERS will be presented. Finally, we provide an overview of analytical SERS with our viewpoints on SERS substrates, approaches to address the analyte generality problem (i.e. target molecules that do not spontaneously adsorb and/or have Raman cross sections <10−29 cm2 sr−1), SERS for catalysis, and deep UV-SERS.

scholarly journals Exosomes in Gliomas: Biogenesis, Isolation, and Preliminary Applications in Nanomedicine

2020 ◽  
Vol 13 (10) ◽  
pp. 319
Author(s):  
Eugenia Romano ◽  
Paolo Antonio Netti ◽  
Enza Torino
Keyword(s):  
Drug Delivery ◽  
Recent Progress ◽  
The Past ◽  
Intracellular Communication ◽  
Isolation Methods ◽  
Potential Applications ◽  
Long Time ◽  
Tumoral Cells ◽  
Brain Malignancy

Exosomes are phospholipid-based particles endogenously produced by both normal and tumor cells. Initially identified as a pathway for shuttling cellular waste, for a long time they were thought to act as “garbage bags”, and only in the past few years have they emerged as a promising drug delivery system. In this review, we provide an overview of the knowledge about exosome architecture and biogenesis and the recent progress in isolation methods. Furthermore, we describe the mechanisms involved in both extra- and intracellular communication with a focus on glioma brain tumors. Glioma is considered a rare disease and is the most prominent aggressive brain malignancy. How exosomes target glial tumoral cells in vivo remains largely unknown. However, they are able to influence numerous physio-pathological aspects. Here, we discuss the role they play in this heterogeneous and complex microenvironment and their potential applications.

scholarly journals Toward Quantitative “In Vivo Biochemistry” with Fluorescence Fluctuation Spectroscopy

2010 ◽  
Vol 21 (24) ◽  
pp. 4306-4311 ◽  
Author(s):  
Brian D. Slaughter ◽  
Rong Li
Keyword(s):  
Protein Dynamics ◽  
Spatial Resolution ◽  
Cell Biology ◽  
Molecular Mechanisms ◽  
Quantitative Description ◽  
Fluorescence Fluctuation Spectroscopy ◽  
Molecular Concentration ◽  
Pros And Cons ◽  
Temporal And Spatial

Quantitative description of protein dynamics and interactions in vivo with temporal and spatial resolution is a key step in dissecting molecular mechanisms in cell biology. Fluorescence fluctuation spectroscopy (FFS) has recently emerged as a powerful in vivo tool for assessing molecular concentration and movement and formation of hetero- and homo-oligomeric complexes. This article discusses point FFS-based analysis methods that have proven useful to cell biologists, focusing on the kinds of information they provide, their pros and cons, and the basic instrumentation required. Along the way, we describe briefly a few recent examples where these analyses have helped address important biological questions.

scholarly journals Robust Sequence Determinants of α-Synuclein Toxicity in Yeast Implicate Membrane Binding

2020 ◽  
Author(s):  
Robert W. Newberry ◽  
Taylor Arhar ◽  
Jean Costello ◽  
George C. Hartoularos ◽  
Alison M. Maxwell ◽  
...  
Keyword(s):  
Structural Model ◽  
Environmental Changes ◽  
Protein Structures ◽  
Yeast Cells ◽  
Cellular Processes ◽  
C Terminus ◽  
Specific Proteins ◽  
Membrane Bound ◽  
Chemical Perturbations

ABSTRACTProtein conformations are shaped by cellular environments, but how environmental changes alter the conformational landscapes of specific proteins in vivo remains largely uncharacterized, in part due to the challenge of probing protein structures in living cells. Here, we use deep mutational scanning to investigate how a toxic conformation of α-synuclein, a dynamic protein linked to Parkinson’s disease, responds to perturbations of cellular proteostasis. In the context of a course for graduate students in the UCSF Integrative Program in Quantitative Biology, we screened a comprehensive library of α-synuclein missense mutants in yeast cells treated with a variety of small molecules that perturb cellular processes linked to α-synuclein biology and pathobiology. We found that the conformation of α-synuclein previously shown to drive yeast toxicity—an extended, membrane-bound helix—is largely unaffected by these chemical perturbations, underscoring the importance of this conformational state as a driver of cellular toxicity. On the other hand, the chemical perturbations have a significant effect on the ability of mutations to suppress α-synuclein toxicity. Moreover, we find that sequence determinants of α-synuclein toxicity are well described by a simple structural model of the membrane-bound helix. This model predicts that α-synuclein penetrates the membrane to constant depth across its length but that membrane affinity decreases toward the C terminus, which is consistent with orthogonal biophysical measurements. Finally, we discuss how parallelized chemical genetics experiments can provide a robust framework for inquiry-based graduate coursework.

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