Unser 10. Leibniz Plant Biochemistry Symposium am 7. und 8. Mai war ein großer Erfolg. Thematisch ging es in diesem Jahr um neue Methoden und Forschungsansätze der Naturstoffchemie. Die exzellenten Vorträge über Wirkstoffe…
Omanische Heilpflanze im Fokus der Phytochemie IPB-Wissenschaftler und Partner aus Dhofar haben jüngst die omanische Heilpflanze Terminalia dhofarica unter die phytochemische Lupe genommen. Die Pflanze ist reich an…
Geschmack ist vorhersagbar: Mit FlavorMiner. FlavorMiner heißt das Tool, das IPB-Chemiker und Partner aus Kolumbien jüngst entwickelt haben. Das Programm kann, basierend auf maschinellem Lernen (KI), anhand der…
Recently, new software tools have been developed for improved protein quantification using mass spectrometry (MS) data. However, there are still limitations especially in high-sample-throughput quantification methods, and most of these relate to extensive computational calculations. The mass accuracy precursor alignment (MAPA) strategy has been shown to be a robust method for relative protein quantification. Its major advantages are high resolution, sensitivity and sample throughput. Its accuracy is data dependent and thus best suited for precursor mass-to-charge precision of ∼1 p.p.m. This protocol describes how to use a software tool (ProtMAX) that allows for the automated alignment of precursors from up to several hundred MS runs within minutes without computational restrictions. It comprises features for 'ion intensity count' and 'target search' of a distinct set of peptides. This procedure also includes the recommended MS settings for complex quantitative MAPA analysis using ProtMAX (http://www.univie.ac.at/mosys/software.html).
Publikation
Dunn, W. B.; Erban, A.; Weber, R. J. M.; Creek, D. J.; Brown, M.; Breitling, R.; Hankemeier, T.; Goodacre, R.; Neumann, S.; Kopka, J.; Viant, M. R.;Mass appeal: metabolite identification in mass spectrometry-focused untargeted metabolomicsMetabolomics944-66(2013)DOI: 10.1007/s11306-012-0434-4
Metabolomics has advanced significantly in the past 10 years with important developments related to hardware, software and methodologies and an increasing complexity of applications. In discovery-based investigations, applying untargeted analytical methods, thousands of metabolites can be detected with no or limited prior knowledge of the metabolite composition of samples. In these cases, metabolite identification is required following data acquisition and processing. Currently, the process of metabolite identification in untargeted metabolomic studies is a significant bottleneck in deriving biological knowledge from metabolomic studies. In this review we highlight the different traditional and emerging tools and strategies applied to identify subsets of metabolites detected in untargeted metabolomic studies applying various mass spectrometry platforms. We indicate the workflows which are routinely applied and highlight the current limitations which need to be overcome to provide efficient, accurate and robust identification of metabolites in untargeted metabolomic studies. These workflows apply to the identification of metabolites, for which the structure can be assigned based on entries in databases, and for those which are not yet stored in databases and which require a de novo structure elucidation.
Publikation
Dekkers, B. J.; Pearce, S.; van Bolderen-Veldkamp, R.; Marshall, A.; Widera, P.; Gilbert, J.; Drost, H.-G.; Bassel, G. W.; Müller, K.; King, J. R.; Wood, A. T.; Grosse, I.; Quint, M.; Krasnogor, N.; Leubner-Metzger, G.; Holdsworth, M. J.; Bentsink, L.;Transcriptional Dynamics of Two Seed Compartments with Opposing Roles in Arabidopsis Seed GerminationPlant Physiol.163205-215(2013)DOI: 10.1104/pp.113.223511
Seed germination is a critical stage in the plant life cycle and the first step toward successful plant establishment. Therefore, understanding germination is of important ecological and agronomical relevance. Previous research revealed that different seed compartments (testa, endosperm, and embryo) control germination, but little is known about the underlying spatial and temporal transcriptome changes that lead to seed germination. We analyzed genome-wide expression in germinating Arabidopsis (Arabidopsis thaliana) seeds with both temporal and spatial detail and provide Web-accessible visualizations of the data reported (vseed.nottingham.ac.uk). We show the potential of this high-resolution data set for the construction of meaningful coexpression networks, which provide insight into the genetic control of germination. The data set reveals two transcriptional phases during germination that are separated by testa rupture. The first phase is marked by large transcriptome changes as the seed switches from a dry, quiescent state to a hydrated and active state. At the end of this first transcriptional phase, the number of differentially expressed genes between consecutive time points drops. This increases again at testa rupture, the start of the second transcriptional phase. Transcriptome data indicate a role for mechano-induced signaling at this stage and subsequently highlight the fates of the endosperm and radicle: senescence and growth, respectively. Finally, using a phylotranscriptomic approach, we show that expression levels of evolutionarily young genes drop during the first transcriptional phase and increase during the second phase. Evolutionarily old genes show an opposite pattern, suggesting a more conserved transcriptome prior to the completion of germination.
Publikation
Chaudhuri, S. R.; Kaluđerović, G. N.; Bette, M.; Schmidt, J.; Schmidt, H.; Paschke, R.; Steinborn, D.;Synthesis, characterization and cytotoxicity studies of platinum(II) complexes with amino acid ligands in various coordination modesInorg. Chim. Acta394472-480(2013)DOI: 10.1016/j.ica.2012.08.034
Reactions of [Pt(CO3)(PPh3)2]·CH2Cl2 (1) with non-substituted and alkyl substituted amino acids, NH(R)CH(R′)CO2H (R/R′ = H/Me, L1; H/iPr, L2; H/CH2CHMe2, L3; Me/H, L4; Et/H, L5), in the presence of Tl[PF6] in methanol afforded with liberation of CO2 the formation of platinum(II) complexes of the type [Pt(PPh3)2{NHR–CHR′–C(O)O-κN,κO}][PF6] (R/R′ = H/Me, 2; H/iPr, 3; H/CH2CHMe2, 4; Me/H, 5; Et/H, 6). Single-crystal X-ray diffraction analysis of complex 4 exhibited a square-planar coordination of the platinum atom having coordinated two triphenylphosphane ligands and a deprotonated κN,κO-coordinated leucine ligand (L3−H). On varying the pKa value of the amino group, platinum(II) complexes with different coordination modes of amino acid ligands were obtained. Thus, treatment of complex 1 with N-acetyl l-alanine (L6), possessing a comparatively highly acidic NH proton, in 1:1 ratio in methanol resulted in the formation of [Pt(PPh3)2{N(COMe)–CHMe–C(O)O-κN,κO}] (7), while reacting N-phenyl glycine (L7) having a moderately acidic NH proton with complex 1 afforded a mixture of complexes [Pt(PPh3)2{NPh–CH2–C(O)O-κN,κO}] (8) and [Pt(PPh3)2{NHPh–CH2–C(O)O-κO}2] (10). Treatment of complex 1 with two equivalents of L6/L7 in dichloromethane resulted in the formation of [Pt(PPh3)2{NHR–CHR′–C(O)O-κO}2] (R/R′ = COMe/Me, 9; Ph/H, 10). An analogous reactivity was observed for l-lactic acid on treating with complex 1 in 1:1 and 2:1 ratio resulting in [Pt(PPh3)2{O–CHMe–C(O)O-κO,κO′}] (11) and [Pt(PPh3)2{HO–CHMe–C(O)O-κO}2] (12). The identities of all complexes have been proven by NMR (1H, 13C, 31P) spectroscopic and high-resolution ESI mass-spectrometric investigations. In vitro cytotoxicity studies against human tumor cell lines (8505C, A2780, HeLa, SW480, and MCF-7) showed the highest activities for the neutral complex 7. Furthermore, complexes 7 and 9 against the A2780 cell line induced an apoptotic mode of cell death, which was further supported by morphological investigation and DNA laddering. Cell cycle perturbation studies showed that both complexes induced faster cell death than cisplatin.