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...

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...

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 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.

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.

scholarly journals Acids Can Promote the Onset and Multimorbidity of Allergic and Nonallergic Airway Diseases

2019 ◽  
Author(s):  
Giuliano Molinari ◽  
Laura Molinari ◽  
Elsa Nervo
Keyword(s):  
Air Pollutants ◽  
Causal Mechanism ◽  
Intracellular Acidification ◽  
Common Cause ◽  
Root Cause ◽  
Airway Diseases ◽  
Biochemical Mechanisms ◽  
The Common ◽  
Airways Inflammation ◽  
In Cells

Inflammatory allergic and nonallergic respiratory pathologies often co-exist. The root cause is not clear. This paper demonstrates that it is ascribable to protons (H+) released into cells by exogenous and endogenous acids. The hypothesis of acids as the common cause stems from two considerations: a) it has long been known that exogenous acids present in air pollutants can induce the irritation of epithelial surfaces, particularly the airways, inflammation and bronchospasm; b) according to recent articles, endogenous acids, generated in cells by phospholipases, play a key role in the biochemical mechanisms of initiation and progression of allergic responses. Therefore, the intracellular acidification and consequent Ca2+ increase, induced by protons generated by either acid pollutants or endogenous phospholipases, may be the causal mechanism of the multimorbidity of these diseases, and environmental acidity may contribute to their spread.

scholarly journals Optochemical Control of Biological Processes in Cells and Animals

2018 ◽  
Vol 57 (11) ◽  
pp. 2768-2798 ◽  
Author(s):  
Nicholas Ankenbruck ◽  
Taylor Courtney ◽  
Yuta Naro ◽  
Alexander Deiters
Keyword(s):  
Biological Processes ◽  
In Cells

scholarly journals The Ste20-like kinase – a Jack of all trades?

2021 ◽  
Vol 134 (9) ◽  
Author(s):  
Brennan Garland ◽  
Samuel Delisle ◽  
Khalid N. Al-Zahrani ◽  
Benjamin R. Pryce ◽  
Luc A. Sabourin
Keyword(s):  
Cancer Progression ◽  
Kinase Activity ◽  
Multiple Roles ◽  
Biological Processes ◽  
Potential Therapeutic Target ◽  
The Past ◽  
Negative Feedback Loops ◽  
Complex Functions ◽  
Cytoskeletal Dynamics ◽  
Biochemical Mechanisms

ABSTRACT Over the past 20 years, the Ste20-like kinase (SLK; also known as STK2) has emerged as a central regulator of cytoskeletal dynamics. Reorganization of the cytoskeleton is necessary for a plethora of biological processes including apoptosis, proliferation, migration, tissue repair and signaling. Several studies have also uncovered a role for SLK in disease progression and cancer. Here, we review the recent findings in the SLK field and summarize the various roles of SLK in different animal models and discuss the biochemical mechanisms regulating SLK activity. Together, these studies have revealed multiple roles for SLK in coupling cytoskeletal dynamics to cell growth, in muscle repair and in negative-feedback loops critical for cancer progression. Furthermore, the ability of SLK to regulate some systems appears to be kinase activity independent, suggesting that it may be an important scaffold for signal transduction pathways. These various findings reveal highly complex functions and regulation patterns of SLK in development and disease, making it a potential therapeutic target.

scholarly journals Molecular probes for cellular imaging of post-translational proteoforms

2022 ◽  
Author(s):  
Surased Suraritdechachai ◽  
Benya Lakkanasirorat ◽  
Chayasith Uttamapinant
Keyword(s):  
Signaling Pathways ◽  
Cellular Imaging ◽  
Molecular Probes ◽  
Biological Processes ◽  
Deep Insight ◽  
Post Translational Modification ◽  
And Function ◽  
Insight Into ◽  
In Cells

Specific post-translational modification (PTM) states of a protein affect its property and function; understanding their dynamics in cells would provide deep insight into diverse signaling pathways and biological processes. However,...

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
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