@article {syhapanha_transcriptomicsguided_2023,
	title = {Transcriptomics-guided identification of an algicidal protease of the marine bacterium Kordia algicida OT-1},
	journal = {MicrobiologyOpen},
	volume = {12},
	number = {5},
	year = {2023},
	pages = {e1387},
	abstract = {In recent years, interest in algicidal bacteria has risen due to their ecological importance and their potential as biotic regulators of harmful algal blooms. Algicidal bacteria shape the plankton communities of the oceans by inhibiting or lysing microalgae and by consuming the released nutrients. Kordia algicida strain OT-1 is a model marine algicidal bacterium that was isolated from a bloom of the diatom Skeletonema costatum. Previous work has suggested that algicidal activity is mediated by secreted proteases. Here, we utilize a transcriptomics-guided approach to identify the serine protease gene KAOT1_RS09515, hereby named alpA1 as a key element in the algicidal activity of K. algicida. The protease AlpA1 was expressed and purified from a heterologous host and used in in vitro bioassays to validate its activity. We also show that K. algicida is the only algicidal species within a group of four members of the Kordia genus. The identification of this algicidal protease opens the possibility of real-time monitoring of the ecological impact of algicidal bacteria in natural phytoplankton blooms., Algicidal bacteria shape the plankton communities of the oceans by lysing microalgae and consuming the released nutrients. Kordia algicida is an environmentally relevant marine bacterium whose algicidal activity is mediated by secreted proteases. In this study, we utilize a transcriptomics-guided approach to identify the secreted serine protease AlpA1 as a key factor in the algicidal process. This discovery offers new approaches for the real-time monitoring and manipulation of algicidal bacteria in algal blooms.},
	keywords = {RCC75},
	issn = {2045-8827},
	doi = {10.1002/mbo3.1387},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10565126/},
	author = {Syhapanha, Kristy S. and Russo, David A. and Deng, Yun and Meyer, Nils and Poulin, Remington X. and Pohnert, Georg}
}
@article {Stettin2020,
	title = {Metabolomics benefits from orbitrap GC{\textendash}MS{\textemdash}Comparison of low- and high-resolution GC{\textendash}MS},
	journal = {Metabolites},
	volume = {10},
	number = {4},
	year = {2020},
	note = {tex.mendeley-tags: RCC75},
	month = {apr},
	pages = {143},
	abstract = {The development of improved mass spectrometers and supporting computational tools is expected to enable the rapid annotation of whole metabolomes. Essential for the progress is the identification of strengths and weaknesses of novel instrumentation in direct comparison to previous instruments. Orbitrap liquid chromatography (LC){\textendash}mass spectrometry (MS) technology is now widely in use, while Orbitrap gas chromatography (GC){\textendash}MS introduced in 2015 has remained fairly unexplored in its potential for metabolomics research. This study aims to evaluate the additional knowledge gained in a metabolomics experiment when using the high-resolution Orbitrap GC{\textendash}MS in comparison to a commonly used unit-mass resolution single-quadrupole GC{\textendash}MS. Samples from an osmotic stress treatment of a non-model organism, the microalga Skeletonema costatum, were investigated using comparative metabolomics with low- and high-resolution methods. Resulting datasets were compared on a statistical level and on the level of individual compound annotation. Both MS approaches resulted in successful classification of stressed vs. non-stressed microalgae but did so using different sets of significantly dysregulated metabolites. High-resolution data only slightly improved conventional library matching but enabled the correct annotation of an unknown. While computational support that utilizes high-resolution GC{\textendash}MS data is still underdeveloped, clear benefits in terms of sensitivity, metabolic coverage, and support in structure elucidation of the Orbitrap GC{\textendash}MS technology for metabolomics studies are shown here.},
	keywords = {Comparative metabolomics, Diatom, High-resolution mass spectrometry (HRMS), Instrument comparison, Mass Spectrometry (Orbitrap GC-MS), Metabolite identification, Orbitrap Gas Chromatography, Osmotic stress, RCC75},
	issn = {2218-1989},
	doi = {10.3390/metabo10040143},
	url = {https://www.mdpi.com/2218-1989/10/4/143},
	author = {Stettin, Daniel and Poulin, Remington X. and Pohnert, Georg}
}
