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09 Feb 2022

Study reveals the protein machinery central to CoQ trafficking in yeast

By nickwiecien

Beyond its role in mitochondrial bioenergetics, Coenzyme Q (CoQ, ubiquinone) serves as a key membrane-embedded antioxidant throughout the cell. However, how CoQ is moved from its site of synthesis on the inner mitochondrial membrane to other sites remains a longstanding mystery. In a recent study, researchers identified two highly conserved but poorly characterized mitochondrial proteins that affect this process. Their results reveal the protein machinery central to CoQ trafficking in yeast and lend insights into the broader interplay between mitochondria and the rest of the cell.

Read the article: UbiB proteins regulate cellular CoQ distribution in Saccharomyces cerevisiae

19 Oct 2021

Mass spectrometry enables sensitive, accurate analysis of neuropeptides

By nickwiecien

Neuropeptides are signaling molecules originating in the neuroendocrine system that can act as neurotransmitters and hormones in many biochemical processes. Their exact function is difficult to know. Mass spectrometry analyses can be used to profile neuropeptide expression changes to understand their roles in many biological problems, such as neurodegenerative disorders and metabolic function.

Read the article: Developing mass spectrometry for the quantitative analysis of neuropeptides.

07 Oct 2021

DiLeu tagging provides insight into human pancreas development

By nickwiecien

The extracellular matrix (ECM) is unique to each tissue, it guides cell differentiation, migration, morphology, and function. It has not been systematically studied in the human pancreas. In this paper, Li et al describe how they used mass spectrometry-based strategies using N,N-dimethyl leucine isobaric tags to identify proteome-wide and ECM-specific alterations in four age groups. They found 3,523 proteins and quantified 117 of them. This work will contribute to understanding the critical roles ECM plays in human pancreas development and maturation.

Read the article: Proteome-wide and matrisome-specific alterations during human pancreas development and maturation

21 Sep 2021

COVID-19: A lesson in community working for the public good

By nickwiecien

In a new longform story, the Morgride Institute of Research scientists and researchers reflect on what collectively happened in late 2019, as the novel coronavirus began spreading and along with it deep uncertainty and unprecedented challenges.

This is a science and also a story about how people and communities came together to work for the public good. It is about the lessons learned and those that still remain. It features the experiences of researchers Tim Grant, Josh Coon, Tony Gitter, Melissa Skala, and Paul Alhquist, and many others.

Read about it here: Resilience: How COVID-19 challenged the scientific world

15 Sep 2021

New features in Coenzyme Q identitifed

By nickwiecien

Coenzyme Q (CoQ), an essential lipid, is manufactured by virtually all cells, but how eukaryotes make the universal CoQ head group precursor 4-hydroxybenzoate (4-HB) from tyrosine is unknown. In this study, Robinson et al. study this pathway with genetic screens, targeted LC-MS, and chemical genetics. The results of their work defines new features of 4-HB synthesis in yeast, demonstrate the redundant nature of this pathway, and provide a foundation for further study.

Read the article: Defining intermediates and redundancies in coenzyme Q precursor biosynthesis

08 Sep 2021

Introducing DiLeuPMP, a multiplexed isobaric labeling method

By nickwiecien

Glycosylation plays an important role in how the human body functions, including cell recognition, signaling, and immune response. While efforts have been devoted to the analysis of N-glycans, high-throughput quantitative analysis of O-glycans is underexplored. In this study, a multiplexed isobaric labeling method, DiLeuPMP, is introduced. This method combines the release and labeling of O-glycans in one step and achieves accurate MS2-based relative quantification. This method provides an effective and reliable approach for the profiling and high-throughput quantitative analysis of O-glycans in complex samples.

Read the article: DiLeuPMP: a multiplexed isobaric labeling method for quantitative analysis of O-glycans

25 Aug 2021

The science behind how soy sauce tastes

By nickwiecien

Soy sauce is a naturally fermented global condiment. It is complex in its chemical profile of salts and organic compounds, but is susceptible to deterioration after bottling. This study by Reddy et al. examined soy sauces over an eight-month period using sensory testing, such as taste and smell, and identifying metabolomic biomarkers using mass spectrometry. They found that changes in soy sauce resulting from storage have decreases in fruity/grape and nutty/sesame taste and aroma, increases in methional/potato aroma and astringent attributes. These taste and smell differences were confirmed with mass spectrometry, which identified changes in the concentrations of several key biomarkers.

Read the article: Metabolomic Biomarkers Differentiate Soy Sauce Freshness under Conditions of Accelerated Storage

18 Aug 2021

Data suggest a unique inflammatory signature associated with severe COVID19

By nickwiecien

The COVID19 pandemic will cause more than a million of deaths worldwide, primarily due to complications from acute respiratory distress syndrome (ARDS). Controversy surrounds the current cytokine/chemokine profile of COVID19-associated ARDS, with some groups suggesting that it is similar to non-COVID19 ARDS patients and others observing substantial differences. Balnis et. al. conducted a study of 41 mechanically ventilated patients with COVID19 infection using highly calibrated methods to define the levels of plasma cytokines/chemokines. Plasma IL1RA and IL8 were found positively associated with mortality, while RANTES and EGF negatively associated with that outcome. However, the leukocyte gene expression of these proteins had no significant correlation with mortality. Their data suggest a unique inflammatory signature associated with severe COVID19.

Read the article: Unique inflammatory profile is associated with higher SARS-CoV-2 acute respiratory distress syndrome (ARDS) mortality

11 Aug 2021

Chemical labeling for glycan and glycopeptide quantitation

By nickwiecien

Growing implications of glycosylation in human disease have prompted intensive focus on revealing glycomic perturbations through absolute and relative quantification. Empowered by an increasing capacity for detection, identification, and characterization, the past decade has provided a significant increase in the number of suitable strategies for glycan and glycopeptide quantification. In this review, Delafield and Li present the most recent advances in chemical labeling and associated techniques for glycan and glycopeptide quantification.

Read the article: Recent Advances in Analytical Approaches for Glycan and Glycopeptide Quantitation

02 Aug 2021

Biologically relevant proteins in Alzheimer’s Disease

By nickwiecien

Proteomic analysis of cerebrospinal fluid (CSF) holds great promise in understanding the progression of neurodegenerative diseases, including Alzheimer’s disease (AD). As one of the primary reservoirs of neuronal biomolecules, CSF provides a window into the biochemical and cellular aspects of the neurological environment. Using mass spectrometry technologies, McKetney et. al. quantified 700 proteins across 10 pairs of age- and sex-matched participants. Using the paired structure, they identified a small group of biologically relevant proteins that show substantial changes in abundance between normal and AD participants. These findings suggest the utility of fractionating a single sample and using matching to increase proteomic depth in CSF.

Read the article: Pilot Proteomic Analysis of Cerebrospinal Fluid in Alzheimer’s Disease. Proteomics Clinical Applications.

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