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New publication looks at the biomarkers of COPD in skeletal muscle integrity response to exercise

A collaboration between the Coon group and the lab of Ariel Jaitovich at Albany Medical College looked at patients with chronic Pulmonary disease (COPD) who developed muscle dysfunction, a condition associated with higher mortality rates and poor outcomes for these individuals. This study was a large-scale analysis of the mouse muscle proteome to identify the significant upregulated proteins contributing to muscle dysfunction.

Read the full article, Established biomarkers of COPD reflect skeletal muscle integrity’s response to exercise in an animal model of pulmonary emphysema, by Balnis et al.

Li lab identifies metabolite and protein biomarkers to identify prostatic inflammation with lower urinary tract symptoms

Lower urinary tract symptoms (LUTS) are common among aging men. Since inflammation is one of its indicators, it is plausible that urinary metabolite and protein biomarkers could be used to identified and diagnose inflammation-induced LUTS. In this study, the Li lab used Mass spectrometry (MS)-based multi-omics analysis to characterize the urine metabolome and proteome in a mouse model. By comparing their findings with urinary biomarkers associated with LUTS in older men, they identified creatine, haptoglobin, immunoglobulin kappa constant and polymeric Ig receptor as conserved biomarkers for prostatic inflammation associated with LUTS.

The full article, Urinary metabolomic and proteomic analyses in a mouse model of prostatic inflammation, can be viewed here.

DiLeu isobaric tags achieves 21-plex quantification

Isobaric tags enable multiplexed quantitative analysis of many biological samples in a single LC-MS/MS experiment. As a cost-effective alternative to expensive commercial isobaric tagging reagents, the lab of Lingjun Li has developed their own custom “DiLeu” isobaric tags for quantitative proteomics. In this paper, Dustin Frost showcases a new generation of DiLeu tags that achieves 21-plex quantification in high-resolution HCD MS/MS spectra.

21-plex DiLeu Isobaric Tags for High-throughput Quantitative Proteomics. Analytical Chemistry.

Li lab collaboration yields insights into spinal cord stimulation for pain relief

A recent publication by Tilley et al titled Proteomic modulation in the dorsal spinal cord following spinal cord stimulation therapy in an in vivo neuropathic pain model, explores how Spinal cord stimulation (SCS) can provide relief for patients suffering from chronic pain, with less dependence on electrical interference. Recent evidence has been growing regarding molecular changes that are induced by SCS as being a key player in reversing the pain process. In this paper the effect of SCS on altering protein expression in spinal cord tissue using a proteomic analysis approach are observed.

Multi-Omics of COVID-19 Collaboration with Albany Medical College

A collaboration with the lab of Dr. Ariel Jaitovich at Albany Medical College studied a Large-scale Multi-omic Analysis of COVID-19 Severity (in preprint). Over 17,000 transcripts, proteins, metabolites, and lipids were quantified and associated with clinical outcomes in a curated relational database, uniquely enabling systems analysis and cross-ome correlations to molecules and patient prognoses. A web-based tool (covid-omics.app) enables interactive exploration and illustrates its utility through a comparative analysis with published data and a machine learning prediction of COVID-19 severity.

Collaboration yields insights into iron restriction for limiting pathogen growth

A recent collaboration titled Tailoring a Global Iron Regulon to a Uropathogen looks at host iron restriction as a mechanism for limiting the growth of pathogens. The study compared the regulatory network controlled by Fur in uropathogenic E. coli (UPEC) to that of nonpathogenic E. coli K-12 to uncover strategies that bacteria use to overcome iron limitation. Although iron homeostasis functions were regulated by Fur in the uropathogen as expected, a surprising finding was the activation of the stringent and general stress responses in the uropathogen fur mutant, which was rescued by amino acid addition. This coordinated global response could be important during transitions from the nutrient-rich environment of the lower gastrointestinal tract to the more restrictive environment of the urinary tract.

Collaboration explores the role of N-glycans during vertebrate development

A collaboration with the lab of Norman Dovichi at the University of Notre Dame explores the role of N-glycans in biological processes during vertebrate development. In a recent publication, Quantitative Capillary Zone Electrophoresis-Mass Spectrometry Reveals the N-glycome Developmental Plan during Vertebrate Embryogenesis, they report on the first quantitative studies of both the expression of N-linked glycans at six early development stages and the expression of N-glycosylated peptides at two early development stages in the African clawed frog. In the study, N-Glycans were labeled with isobaric tandem mass tags and characterized using tandem mass spectrometry. Over two thirds of the N-glycoproteins identified in the late stage were associated with neuron projection morphogenesis, suggesting a vital role of the N-glycome in neuronal development.

Collaboration with Puglielli lab reveals AT-1 acts as metabolic regulator for acetyl-CoA

In a paper titled Acetyl-CoA Flux Regulates the Proteome and Acetyl-Proteome to Maintain Intracellular Metabolic Crosstalk, Inca Dieterich et al. of Prof Luigi Puglielli’s lab investigated two models of AT-1 dysregulation and altered acetyl-CoA flux: AT-1S113R/+ mice, a model of AT-1 haploin sufficiency, and AT-1 sTg mice, a model of AT-1 overexpression. The animals display distinct metabolic adaptation across intracellular compartments, including reprogramming of lipid metabolism and mitochondria bioenergetics. Our results suggest that AT-1 acts as an important metabolic regulator that maintains acetyl-CoA homeostasis by promoting functional crosstalk between different intracellular organelles.

Recent research shows activated ion electron transfer dissociation has better performance for proteoform fragmentation

Elijah McCool, a graduate student in Lab of Dr. Liangliang Sun at Michigan State University, recently published on a collaboration with NCBBCS, Capillary Zone Electrophoresis-Tandem Mass Spectrometry with Activated Ion Electron Transfer Dissociation for Large-scale Top-down Proteomics. in the Journal of The American Society for Mass Spectrometry.

Capillary zone electrophoresis-tandem mass spectrometry is recognized as an efficient approach for top-down proteomics because of its high-capacity separation and highly sensitive detection of proteoforms. However, the commonly used collision-based methods often don’t provide the extensive fragmentation needed for thorough characterization of proteoforms. Activated ion electron transfer dissociation (AI-ETD), which combines infrared photoactivation with ETD, has shown better performance for proteoform fragmentation than other methods.

Collaboration Yields Insight on Role of Metabolism in Bacterial Growth

Bacterial biofilms are everywhere in nature and play an important role in many clinical, industrial, and ecological settings. Although much is known about the transcriptional regulatory networks that control biofilm formation in model bacteria such as Bacillus subtilis, very little is known about the role of metabolism in this process. To address this important knowledge gap, this study used a time-resolved analysis of the metabolic changes associated with bacterial biofilm development in B. subtilis by combining metabolomic, transcriptomic, and proteomic analyses. This report serves as a unique resource for future studies and will be relevant to future research in microbial physiology and metabolism. The full publication can be found here.