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Publications - Stress and Develop Biology

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Sheikh, A.H.; Raghuram, B.; Eschen-Lippold, L.; Scheel, D.; Lee, J.; Sinha, A.K. Agroinfiltration by cytokinin-producing Agrobacterium strain GV3101 primes defense responses in Nicotiana tabacum. Mol Plant Microbe Interact 27, 1175-1185, (2014) DOI: 10.1094/MPMI-04-14-0114-R

Transient infiltrations in tobacco are commonly used in plant studies but the host response to different disarmed Agrobacterium strains is not fully understood. The present study shows that the pre-treatment with disarmed Agrobacterium tumefaciens strain GV3101 primes the defense response to subsequent infection by Pseudomonas syringae in Nicotiana tabacum. The presence of a trans-zeatin synthase (tzs) gene in strain GV3101 may be partly responsible for the priming response as the tzs deficient Agrobacterium strain LBA4404 only weakly imparts such responses. Besides inducing the expression of defense-related genes like PR-1 and NHL10, GV3101 pre-treatment increased the expression of tobacco mitogen-activated protein kinase pathway genes like MEK2, WIPK and SIPK . Furthermore, the GV3101 strain showed a stronger effect than the LBA4404 strain in activating phosphorylation of the tobacco MAP kinases, WIPK and SIPK, which presumably primes the plant immune machinery. Lower doses of exogenously applied cytokinins increased the activation of MAPKs while higher doses decreased the activation, suggesting a balanced level of cytokinins is required to generate defense response in planta. The current study serves as a cautionary warning for plant researchers over the choice of Agrobacterium strains and their possible consequences on subsequent pathogen-related studies.

Rasche, F.; Svatoš, A.; Maddula, R. K.; Böttcher, C.; Böcker, S. Computing Fragmentation Trees from Tandem Mass Spectrometry Data Anal Chem 83, 1243-1251, (2011) DOI: 10.1021/ac101825k

The structural elucidation of organic compounds in complex biofluids and tissues remains a significant analytical challenge. For mass spectrometry, the manual interpretation of collision-induced dissociation (CID) mass spectra is cumbersome and requires expert knowledge, as the fragmentation mechanisms of ions formed from small molecules are not completely understood. The automated identification of compounds is generally limited to searching in spectral libraries. Here, we present a method for interpreting the CID spectra of the organic compound’s protonated ions by computing fragmentation trees that establish not only the molecular formula of the compound and all fragment ions but also the dependencies between fragment ions. This is an important step toward the automated identification of unknowns from the CID spectra of compounds that are not in any database.
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