nickwiecien

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Study reveals the protein machinery central to CoQ trafficking in yeast

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

New plasma protocol for LC-MS/MS

Evgenia Shishkova has developed a new protocol that offers step-by-step instructions for preparation of raw blood plasma for liquid chromatography – tandem mass spectrometry (LC-MS/MS). The technique is simple, robust, and reproducible. The entire transformation only takes 3–4 h. This protocol can be adopted for large-scale studies and automation.

Process is available in STAR Protocols: Rapid preparation of human blood plasma for bottom-up proteomics analysis

New study asks “Do oral diseases correlate with other health outcomes?”

The human mouth harbors a wide variety of microbes – over 700 kinds. These bacteria are in saliva, on the tongue and cheeks, on the tooth surface and under the gums. The development of plaque is particularly important in diseases like tooth decay and gum disease. The oral microbiota that contribute to these disease are also correlated with other diseases, including diabetes, arthritis, and heart disease, suggesting they have a broad impact on human health. This study analyzed the microbiome, proteome, lipidome, and metabolome of dental plaque samples from individuals with periodontal disease and pre- and type 2 diabetes.

Read the article: Proteomics, lipidomics, metabolomics and 16S rDNA sequencing of dental plaque from patients with diabetes and periodontal disease.

Read the article: Proteomics, lipidomics, metabolomics and 16S rDNA sequencing of dental plaque from patients with diabetes and periodontal disease

Mass spectrometry enables sensitive, accurate analysis of neuropeptides

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.

DiLeu tagging provides insight into human pancreas development

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

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

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

New features in Coenzyme Q identitifed

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

Introducing DiLeuPMP, a multiplexed isobaric labeling method

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

The science behind how soy sauce tastes

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