Proteomics最新文献

As space exploration becomes increasingly accessible, understanding the molecular and pathophysiological consequences of spaceflight on the human body becomes crucial. Space-induced modifications could disrupt multiple signaling pathways, with significant implications for the functional integrity of cardiovascular, nervous, and musculoskeletal systems, among others. In a recent study, Bourdakou et al. have focused on alterations in gene expression profiles linked to cardiovascular disease (CVD), using human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) undergoing spaceflight and subsequent postflight conditions. Genes with known associations with CVD and nuclear factor erythroid 2-related factor 2 (NRF2) oxidative stress regulatory network have been identified to present consistent directional expression changes in both spaceflight and postflight. A computational drug repurposing analysis identified ten candidate agents with the potential to reverse observed transcriptomic modifications in spaceflight-exposed cardiomyocytes. These findings highlight the importance of molecular studies and emphasize the need for integrative, multi-omic research efforts to protect human health during and beyond spaceflight.

The cochlea, an incredibly sensitive sensory system, detects sound waves and converts them into electrical signals the brain recognizes as sound. Damage to cochlear hair cells can release proteins, triggering biological responses that may impair hearing. Mass spectrometry-based proteomics offers insights into protein expression changes in cochlear tissues, improving our understanding of inner ear diseases. In this study, we performed a comprehensive proteomics analysis of whole cochlear tissue extracted from healthy guinea pigs and rats. The study optimized protein extraction protocols and analyzed cochlear protein expression using three biological replicates for each animal model. The results included the identification of 1841 proteins in guinea pigs and 3423 proteins in rats, with a high overlap in cochlear protein expression between the left and right ears—93% in guinea pigs and 89% in rats. The findings validate the assumption that the cochlear tissues from both sides of the ears can be considered biologically equivalent. This experiment provides a comprehensive cochlear proteome for guinea pigs and rats, supporting future studies on inner ear disorders.

Increasing global food production demands have resulted in increased fertilizer usage, causing detrimental environmental impacts. Biostimulants, such as humic substances, are currently being applied as a strategy to increase plant nutrient-use efficiency and minimize environmental impacts within cropping systems. One of these biostimulants is Humalite, which is a unique, naturally occurring coal-like substance found in deposits across southern Alberta. These deposits contain exceptionally high ratios of humic acids (>70%) and micronutrients due to their unique freshwater depositional environment. Humalite has begun to be applied to fields based on scientific data suggesting positive impacts on crop growth, yield, and nutrient usage; however, little is known about the underlying molecular mechanisms of Humalite. Here, as part of a larger field study, we report a quantitative proteomics approach to identify systems-level molecular changes induced by the addition of different Humalite application rates in field-grown wheat (Triticum aestivum L.) under three urea fertilizer application rates. In particular, we see wide-ranging abundance changes in proteins associated with several metabolic pathways and growth-related biological processes that suggest how Humalite modulates the plant molecular landscape. Overall, our results provide new, functional information that will help better inform agricultural producers on optimal biostimulant and fertilizer usage.

Phytoplankton blooms create a substrate-rich environment that supports the growth of bacterial planktonic heterotrophs. Previously, we studied the dynamics of such bacterioplankton at a long-term ecological research site near the coast of Helgoland Island (North Sea) once a day. Here, we present a novel dataset (available under the PRIDE-ID: PXD055396) indicating significant differences at the protein level in a semi-diurnal analysis. Using metaproteomics, we studied changes in the free-living (0.2–3 µm) bacterial community that occurred between early (7 am) and late (9 pm) sampling over 3 days. The results highlight the sensitivity, robustness, and reproducibility of mass spectrometry-based metaproteomic analyses to assess changes in the activities of the bacterioplankton communities. Taxonomic analyses revealed significant changes in the abundance of 65 bacterial genera. Particularly, proteins from the flavobacterial genera Candidatus Prosiliicoccus and Aurantivirga were significantly more abundant in the late samples. This comprehensive dataset highlights semi-diurnal changes in bacterial community composition and metabolic activity during a phytoplankton bloom that would have remained undetected with a once-per-day sampling approach.

Advances in methodologies and technologies over the past decade have led to an unprecedented depth of analysis of a cell's biomolecules, with entire genomes able to be sequenced in hours and up to 10,000 transcripts or ORF products (proteins) able to be quantified from a single cell. Methods for analysing individual omes are now optimised, reliable and robust but are often performed in isolation with other biomolecules considered contaminants. However, there is a growing body of systems biology studies that aim to study multiple omes from the same sample. This review details the current state of the “multi-omics” field, trying to define what the field is, the methodologies employed and the challenges facing researchers in this field. It also critically evaluates whether these approaches are “fit-for-purpose” and how the field needs to evolve to enhance our understanding of how biomolecules from distinct omes interact with one another to alter cellular phenotype in response to change.

Detergents are key reagents in bottom-up proteomics that create an apparent, yet underappreciated bias on observable proteomes. Maximizing the chemical diversity of detergents in parallelized screens is supposed to maximize observable proteomes if proteomics data sets of different detergents are combined. The aim of our work is to investigate the potential of fusing ionic and nonionic detergent headgroups into hybrid detergents for increasing the observable number of unique protein identities. Our data indicate that the solubilizing properties of hybrid detergents do not reflect an average of canonical detergents. The number of unique protein identities obtainable from an Escherichia coli screen increases from 1604 to 2169 when proteomics data sets from sodium dodecyl sulfate, dodecyltrimethylammonium bromide, dendritic triglycerol detergent, and related hybrid detergents are combined. Our data highlight the utility of cationic detergents and related hybrid detergents for enhancing observable proteomes. Detergent screening–based proteome reconstructions with canonical detergents and hybrid detergents present an interesting research direction towards improved proteome profiling applications.