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…
Seit Februar 2021 bietet Wolfgang Brandt, ehemaliger Leiter der Arbeitsgruppe Computerchemie am IPB, sein Citizen Science-Projekt zur Pilzbestimmung an. Dafür hat er in regelmäßigen Abständen öffentliche Vorträge zur Vielfalt…
Results of scientific work in chemistry can usually be obtained in the form of materials and data. A big step towards transparency and reproducibility of the scientific work can be gained if scientists publish their data in research data repositories in a FAIR manner. Nevertheless, in order to make chemistry a sustainable discipline, obtaining FAIR data is insufficient and a comprehensive concept that includes preservation of materials is needed. In order to offer a comprehensive infrastructure to find and access data and materials that were generated in chemistry projects, we combined the infrastructure Chemotion repository with an archive for chemical compounds. Samples play a key role in this concept: we describe how FAIR metadata of a virtual sample representation can be used to refer to a physically available sample in a materials’ archive and to link it with the FAIR research data gained using the said sample. We further describe the measures to make the physically available samples not only FAIR through their metadata but also findable, accessible and reusable.
Publikation
Klein, J.; Lam, H.; Mak, T. D.; Bittremieux, W.; Perez-Riverol, Y.; Gabriels, R.; Shofstahl, J.; Hecht, H.; Binz, P.-A.; Kawano, S.; Van Den Bossche, T.; Carver, J.; Neely, B. A.; Mendoza, L.; Suomi, T.; Claeys, T.; Payne, T.; Schulte, D.; Sun, Z.; Hoffmann, N.; Zhu, Y.; Neumann, S.; Jones, A. R.; Bandeira, N.; Vizcaíno, J. A.; Deutsch, E. W.;The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: mzSpecLib and mzPAFAnal. Chem.9618491-18501(2024)DOI: 10.1021/acs.analchem.4c04091
Mass spectral libraries are collections of reference spectra, usually associated with specific analytes from which the spectra were generated, that are used for further downstream analysis of new spectra. There are many different formats used for encoding spectral libraries, but none have undergone a standardization process to ensure broad applicability to many applications. As part of the Human Proteome Organization Proteomics Standards Initiative (PSI), we have developed a standardized format for encoding spectral libraries, called mzSpecLib (https://psidev.info/mzSpecLib). It is primarily a data model that flexibly encodes metadata about the library entries using the extensible PSI-MS controlled vocabulary and can be encoded in and converted between different serialization formats. We have also developed a standardized data model and serialization for fragment ion peak annotations, called mzPAF (https://psidev.info/mzPAF). It is defined as a separate standard, since it may be used for other applications besides spectral libraries. The mzSpecLib and mzPAF standards are compatible with existing PSI standards such as ProForma 2.0 and the Universal Spectrum Identifier. The mzSpecLib and mzPAF standards have been primarily defined for peptides in proteomics applications with basic small molecule support. They could be extended in the future to other fields that need to encode spectral libraries for nonpeptidic analytes.
Publikation
Clúa, J.; Montpetit, J.; Jimenez-Sandoval, P.; Naumann, C.; Santiago, J.; Poirier, Y.;A CYBDOM protein impacts iron homeostasis and primary root growth under phosphate deficiency in ArabidopsisNat. Commun.15423(2024)DOI: 10.1038/s41467-023-43911-x
Arabidopsis primary root growth response to phosphate (Pi) deficiency is mainly controlled by changes in apoplastic iron (Fe). Upon Pi deficiency, apoplastic Fe deposition in the root apical meristem activates pathways leading to the arrest of meristem maintenance and inhibition of cell elongation. Here, we report that a member of the uncharacterized cytochrome b561 and DOMON domain (CYBDOM) protein family, named CRR, promotes iron reduction in an ascorbate-dependent manner and controls apoplastic iron deposition. Under low Pi, the crr mutant shows an enhanced reduction of primary root growth associated with increased apoplastic Fe in the root meristem and a reduction in meristematic cell division. Conversely, CRR overexpression abolishes apoplastic Fe deposition rendering primary root growth insensitive to low Pi. The crr single mutant and crr hyp1 double mutant, harboring a null allele in another member of the CYDOM family, shows increased tolerance to high-Fe stress upon germination and seedling growth. Conversely, CRR overexpression is associated with increased uptake and translocation of Fe to the shoot and results in plants highly sensitive to Fe excess. Our results identify a ferric reductase implicated in Fe homeostasis and developmental responses to abiotic stress, and reveal a biological role for CYBDOM proteins in plants.
Publikation
Abel, S.; Naumann, C.;Evolution of phosphate scouting in the terrestrial biospherePhilosophical Transactions of the Royal Society B: Biological Sciences37920230355(2024)DOI: 10.1098/rstb.2023.0355
Chemistry assigns phosphorus and its most oxidized form, inorganic phosphate, unique roles for propelling bioenergetics and metabolism in all domains of life, possibly since its very origin on prebiotic Earth. For plants, access to the vital mineral nutrient profoundly affects growth, development and vigour, thus constraining net primary productivity in natural ecosystems and crop production in modern agriculture. Unlike other major biogenic elements, the low abundance and uneven distribution of phosphate in Earth’s crust result from the peculiarities of phosphorus cosmochemistry and geochemistry. Here, we trace the chemical evolution of the element, the geochemical phosphorus cycle and its acceleration during Earth’s history until the present (Anthropocene) as well as during the evolution and rise of terrestrial plants. We highlight the chemical and biological processes of phosphate mobilization and acquisition, first evolved in bacteria, refined in fungi and algae and expanded into powerful phosphate-prospecting strategies during land plant colonization. Furthermore, we review the evolution of the genetic and molecular networks from bacteria to terrestrial plants, which monitor intracellular and extracellular phosphate availabilities and coordinate the appropriate responses and adjustments to fluctuating phosphate supply. Lastly, we discuss the modern global phosphorus cycle deranged by human activity and the challenges imposed ahead.
This article is part of the theme issue ‘Evolution and diversity of plant metabolism’.