Label-free hyperspectral microscopy for scatter imaging of biological processes in cells (Conference Presentation)

2016 ◽  
Author(s):  
Jeeseong C. Hwang ◽  
Aniruddha Ray ◽  
Philip P. Cheney ◽  
Bonghwan Chon ◽  
Ji Youn Lee ◽  
...  
Keyword(s):  
Biological Processes ◽  
Label Free ◽  
In Cells

Mitochondria-targeting fluorescent sensor for on-off-on response to Cu2+ and ATP in cells and zebrafish

The Analyst ◽  
2021 ◽  
Author(s):  
Wan Sun ◽  
Guofeng Liu ◽  
Mingqiong Tong ◽  
Haozhan Wang ◽  
Shuhan Liu
Keyword(s):  
Adenosine Triphosphate ◽  
Fluorescent Sensor ◽  
Biological Processes ◽  
Fluorescent Molecule ◽  
Cupric Ion ◽  
Mitochondria Targeting ◽  
In Cells

Cupric ion (Cu2+) and adenosine triphosphate (ATP) are functionally important in mitochondria and play essential roles in many important biological processes. In this work, a mitochondria-targeting fluorescent molecule Mito-A was...

Interrogating the Transcriptome with Metabolically Incorporated Ribonucleosides

2021 ◽  
Author(s):  
Ralph Kleiner
Keyword(s):  
Biological Processes ◽  
Biochemical Mechanisms ◽  
In Cells

RNA is a central player in biological processes, but there remain major gaps in our understanding of transcriptomic processes and the underlying biochemical mechanisms regulating RNA in cells. A powerful...

Glycan Labeling and Analysis in Cells and In Vivo

2021 ◽  
Vol 14 (1) ◽  
pp. 363-387
Author(s):  
Bo Cheng ◽  
Qi Tang ◽  
Che Zhang ◽  
Xing Chen
Keyword(s):  
Chemical Modification ◽  
Biological Function ◽  
Biological Processes ◽  
Affinity Tags ◽  
Functional Roles ◽  
Antibody Conjugates ◽  
Living Organisms ◽  
In Cells

As one of the major types of biomacromolecules in the cell, glycans play essential functional roles in various biological processes. Compared with proteins and nucleic acids, the analysis of glycans in situ has been more challenging. Herein we review recent advances in the development of methods and strategies for labeling, imaging, and profiling of glycans in cells and in vivo. Cellular glycans can be labeled by affinity-based probes, including lectin and antibody conjugates, direct chemical modification, metabolic glycan labeling, and chemoenzymatic labeling. These methods have been applied to label glycans with fluorophores, which enables the visualization and tracking of glycans in cells, tissues, and living organisms. Alternatively, labeling glycans with affinity tags has enabled the enrichment of glycoproteins for glycoproteomic profiling. Built on the glycan labeling methods, strategies enabling cell-selective and tissue-specific glycan labeling and protein-specific glycan imaging have been developed. With these methods and strategies, researchers are now better poised than ever to dissect the biological function of glycans in physiological or pathological contexts.

scholarly journals Systematic Enzyme Mapping of Cellular Metabolism by Phasor-Analyzed Label-Free NAD(P)H Fluorescence Lifetime Imaging

2019 ◽  
Vol 20 (22) ◽  
pp. 5565 ◽  
Author(s):  
Leben ◽  
Köhler ◽  
Radbruch ◽  
Hauser ◽  
Niesner
Keyword(s):  
Fluorescence Lifetime ◽  
Metabolic Activity ◽  
Cellular Metabolism ◽  
Fluorescence Lifetime Imaging ◽  
Label Free ◽  
Analysis Framework ◽  
Cell Nuclei ◽  
Lifetime Imaging ◽  
Subcellular Resolution ◽  
In Cells

In the past years, cellular metabolism of the immune system experienced a revival, as it has become clear that it is not merely responsible for the cellular energy supply, but also impacts on many signaling pathways and, thus, on diverse cellular functions. Label-free fluorescence lifetime imaging of the ubiquitous coenzymes NADH and NADPH (NAD(P)H-FLIM) makes it possible to monitor cellular metabolism in living cells and tissues and has already been applied to study metabolic changes both under physiologic and pathologic conditions. However, due to the complex distribution of NAD(P)H-dependent enzymes in cells, whose distribution continuously changes over time, a thorough interpretation of NAD(P)H-FLIM results, in particular, resolving the contribution of various enzymes to the overall metabolic activity, remains challenging. We developed a systematic framework based on angle similarities of the phase vectors and their length to analyze NAD(P)H-FLIM data of cells and tissues based on a generally valid reference system of highly abundant NAD(P)H-dependent enzymes in cells. By using our analysis framework, we retrieve information not only about the overall metabolic activity, i.e., the fraction of free to enzyme-bound NAD(P)H, but also identified the enzymes predominantly active within the sample at a certain time point with subcellular resolution. We verified the performance of the approach by applying NAD(P)H-FLIM on a stromal-like cell line and identified a different group of enzymes that were active in the cell nuclei as compared to the cytoplasm. As the systematic phasor-based analysis framework of label-free NAD(P)H-FLIM can be applied both in vitro and in vivo, it retains the unique power to enable dynamic enzyme-based metabolic investigations, at subcellular resolution, in genuine environments.

scholarly journals The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST)

2020 ◽  
Author(s):  
Vasundra Touré ◽  
Steven Vercruysse ◽  
Marcio Luis Acencio ◽  
Ruth C Lovering ◽  
Sandra Orchard ◽  
...  
Keyword(s):  
Molecular Interaction ◽  
Regulatory Networks ◽  
Building Blocks ◽  
Supplementary Information ◽  
Biological Processes ◽  
Causal Interaction ◽  
End User ◽  
Minimum Information ◽  
Causal Statement ◽  
In Cells

Abstract Motivation A large variety of molecular interactions occurs between biomolecular components in cells. When a molecular interaction results in a regulatory effect, exerted by one component onto a downstream component, a so-called ‘causal interaction’ takes place. Causal interactions constitute the building blocks in our understanding of larger regulatory networks in cells. These causal interactions and the biological processes they enable (e.g. gene regulation) need to be described with a careful appreciation of the underlying molecular reactions. A proper description of this information enables archiving, sharing and reuse by humans and for automated computational processing. Various representations of causal relationships between biological components are currently used in a variety of resources. Results Here, we propose a checklist that accommodates current representations, called the Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). This checklist defines both the required core information, as well as a comprehensive set of other contextual details valuable to the end user and relevant for reusing and reproducing causal molecular interaction information. The MI2CAST checklist can be used as reporting guidelines when annotating and curating causal statements, while fostering uniformity and interoperability of the data across resources. Availability and implementation The checklist together with examples is accessible at https://github.com/MI2CAST/MI2CAST Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Proteomic Profiles and Biological Processes of Relapsed vs. Non-Relapsed Pediatric Hodgkin Lymphoma

2020 ◽  
Vol 21 (6) ◽  
pp. 2185
Author(s):  
Ombretta Repetto ◽  
Valli De Re ◽  
Lara Mussolin ◽  
Massimo Tedeschi ◽  
Caterina Elia ◽  
...  
Keyword(s):  
Hodgkin Lymphoma ◽  
Gel Electrophoresis ◽  
Predictive Biomarkers ◽  
Biological Processes ◽  
Label Free ◽  
Pediatric Hodgkin Lymphoma ◽  
Difference Gel Electrophoresis ◽  
Thrombospondin 1 ◽  
Serum Paraoxonase ◽  
Differentially Abundant Proteins

The identification of circulating proteins associated with relapse in pediatric Hodgkin lymphoma (HL) may help develop predictive biomarkers. We previously identified a set of predictive biomarkers by difference gel electrophoresis. Here we used label-free quantitative liquid chromatography-mass spectrometry (LC-MS/MS) on plasma collected at diagnosis from 12 children (age 12–16 years) with nodular sclerosis HL, including six in whom the disease relapsed within 5 years of treatment in the LH2004 trial. Plasma proteins were pooled in groups of three, separately for non-relapsing and relapsing HL, and differentially abundant proteins between the two disease states were identified by LC-MS/MS in an explorative and validation design. Proteins with a fold change in abundance >1.2 or ≤0.8 were considered “differentially abundant”. LC-MS/MS identified 60 and 32 proteins that were more abundant in non-relapsing and relapsing HL plasma, respectively, in the explorative phase; these numbers were 39 and 34 in the validation phase. In both analyses, 11 proteins were more abundant in non-relapsing HL (e.g., angiotensinogen, serum paraoxonase/arylesterase 1, transthyretin), including two previously identified by difference gel electrophoresis (antithrombin III and α-1-antitrypsin); seven proteins were more abundant in relapsing HL (e.g., fibronectin and thrombospondin-1), including two previously identified proteins (fibrinogen β and γ chains). The differentially abundant proteins participated in numerous biological processes, which were manually grouped into 10 biological classes and 11 biological regulatory subclasses. The biological class Lipid metabolism, and its regulatory subclass, included angiotensinogen and serum paraoxonase/arylesterase 1 (more abundant in non-relapsing HL). The biological classes Immune system and Cell and extracellular matrix architecture included fibronectin and thrombospondin-1 (more abundant in relapsing HL). These findings deepen our understanding of the molecular scenario underlying responses to therapy and provide new evidence about these proteins as possible biomarkers of relapse in pediatric HL.

Label-free imaging of semiconducting and metallic carbon nanotubes in cells and mice using transient absorption microscopy

2011 ◽  
Vol 7 (1) ◽  
pp. 56-61 ◽  
Author(s):  
Ling Tong ◽  
Yuxiang Liu ◽  
Bridget D. Dolash ◽  
Yookyung Jung ◽  
Mikhail N. Slipchenko ◽  
...  
Keyword(s):  
Carbon Nanotubes ◽  
Transient Absorption ◽  
Label Free ◽  
In Cells

A review: the trend of progress about pH probes in cell application in recent years

The Analyst ◽  
2017 ◽  
Vol 142 (1) ◽  
pp. 30-41 ◽  
Author(s):  
Yongkang Yue ◽  
Fangjun Huo ◽  
Songyi Lee ◽  
Caixia Yin ◽  
Juyoung Yoon
Keyword(s):  
Intracellular Ph ◽  
Body Fluids ◽  
The Body ◽  
Biological Processes ◽  
Acid Base ◽  
Ph Values ◽  
Ph Probes ◽  
In Cells

Intracellular pH values are some of the most important factors that govern biological processes and the acid–base homeostasis in cells, body fluids and organs sustains the normal operations of the body.

Sign in / Sign up

Export Citation Format

Share Document