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Li lab collaboration explores noninvasive markers in prostate disease diagnosis

A recent collaboration between the labs of Lingjun Li and William Ricke explores the relationship between prostatic hyperplasia and related lower urinary tract symptoms in aging males and how noninvasive markers could be helpful in disease diagnosis. This proteomics study used a mouse model of hormone-induced urinary dysfunction to gain insight into the disease and supports the concept of noninvasive urinary biomarkers being a successful route for prostate disease diagnostics.

Thomas S, Hao L, DeLaney K, McLean D, Steinke L, Marker PC, Vezina CM, Li L, Ricke WA. Spatiotemporal proteomics reveals the molecular consequences of hormone treatment in a mouse model of lower urinary tract dysfunction. Journal of Proteome Research. 2020, 19(4):1375-1382.

Characterizing modified nucleic acids using negative electron transfer dissociation

A recent publication in Analytical Chemistry by Trenton Peters-Clarke explores the promise of modified oligonucleotides for drug development, with small interfering RNAs (siRNA) and microRNAs gaining traction in the therapeutic market. Mass spectrometry (MS)-based analysis offers many benefits for characterizing modified nucleic acids. Negative electron transfer dissociation (NETD) has proven valuable in sequencing oligonucleotide anions, particularly because it can retain modifications while generating sequence-informative fragments.

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.


If you are attending the virtual ASMS conference June 1-12, 2020, please join the presentations by NCQBCS faculty and graduate students:

Tuesday Prof. Lingjun Li will chair a session on Glycopeptides and Glycoproteins from 02:30- 04:10 pm (TOG) and graduate student Trenton Peters-Clarke will present “Ribonucleic Acid Sequence Characterization by Activated Ion-Negative Electron Transfer Dissociation (AI-NETD) Mass Spectrometry.” (TOF 02:50pm)

On Thursday, graduate student Gongyu Li will present “Millisecond Chiral Separation by Multidimensional IM-MS Provides Molecular and Structural Basis for Next-generation Therapy of Alzheimer’s Disease” (ThOB pm 02:50).

Hope you can join us!

Collaboration with Burkard Lab Explores Polo-like Kinase Substrates

Johnson et al (2020) explore chemically controlling substrates through toggling.

Polo-like kinase 1 has hundreds of substrates and multiple functions that operate within the ∼60 min of mitosis. This paper describes a chemical-genetic system that allows particular substrates to be “toggled” into or out of chemical control using engineered phosphoacceptor selectivity. Kif2b, a known substrate of Plk1 that regulates chromosome alignment was evaluated. Toggling Ser to Thr on Kif2b places these phosphorylation sites under reversible chemical control. Thus, it is demonstrated the ability to chemically control a single substrate by a genetic Ser/Thr toggle.

Glycoproteome and Surfaceome Changes in Isogenic Cells

Leung et al (2020) investigated key cell surface regions and their interactions with the extracellular environment in order to understand how to develop possible cancer immunotherapy drugs in a recent issue of Proceedings of the National Academy of Sciences.

Specifically, in order to understand how oncogenes remodel isogenic cells, researchers conducted quantitative proteomics on N-linked glycoproteins. Here, researchers observed how a large number of surface proteins were changed in isogenic breast epithelial cell lines to express oncogenes.

In addition to looking at surfaceome data with applied glycoproteoics, researchers also applied activated ion electron transfer dissociation (AI-ETD). Here. researchers found changes to the glycoproteome, as induced by the oncogenes.

Researchers said that these studies could help illustrate how specific oncogenes can remodel both the surfaceome and the glycoproteome in cells. Additionally, this research can help in the production of further cancer antibody drug discovery research.

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