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…
Khalil, S.; Strah, R.; Lodovici, A.; Vojta, P.; Berardinis, F. D.; Ziegler, J.; Novak, M. P.; Zanin, L.; Tomasi, N.; Forneck, A.; Griesser, M.;The activation of iron deficiency responses of grapevine rootstocks is dependent to the availability of the nitrogen formsBMC Plant Biol.24218(2024)DOI: 10.1186/s12870-024-04906-y
Background
In viticulture, iron (Fe) chlorosis is a common abiotic stress that impairs plant development and leads to yield and quality losses. Under low availability of the metal, the applied N form (nitrate and ammonium) can play a role in promoting or mitigating Fe deficiency stresses. However, the processes involved are not clear in grapevine. Therefore, the aim of this study was to investigate the response of two grapevine rootstocks to the interaction between N forms and Fe uptake. This process was evaluated in a hydroponic experiment using two ungrafted grapevine rootstocks Fercal (Vitis berlandieri x V. vinifera) tolerant to deficiency induced Fe chlorosis and Couderc 3309 (V. riparia x V. rupestris) susceptible to deficiency induced Fe chlorosis.
Results The results could differentiate Fe deficiency effects, N-forms effects, and rootstock effects. Interveinal chlorosis of young leaves appeared earlier on 3309 C from the second week of treatment with NO3−/NH4+ (1:0)/-Fe, while Fercal leaves showed less severe symptoms after four weeks of treatment, corresponding to decreased chlorophyll concentrations lowered by 75% in 3309 C and 57% in Fercal. Ferric chelate reductase (FCR) activity was by trend enhanced under Fe deficiency in Fercal with both N combinations, whereas 3309 C showed an increase in FCR activity under Fe deficiency only with NO3−/NH4+ (1:1) treatment. With the transcriptome analysis, Gene Ontology (GO) revealed multiple biological processes and molecular functions that were significantly regulated in grapevine rootstocks under Fe-deficient conditions, with more genes regulated in Fercal responses, especially when both forms of N were supplied. Furthermore, the expression of genes involved in the auxin and abscisic acid metabolic pathways was markedly increased by the equal supply of both forms of N under Fe deficiency conditions. In addition, changes in the expression of genes related to Fe uptake, regulation, and transport reflected the different responses of the two grapevine rootstocks to different N forms.
Conclusions Results show a clear contribution of N forms to the response of the two grapevine rootstocks under Fe deficiency, highlighting the importance of providing both N forms (nitrate and ammonium) in an appropriate ratio in order to ease the rootstock responses to Fe deficiency.
Publikation
Jozwiak, A.; Panda, S.; Akiyama, R.; Yoneda, A.; Umemoto, N.; Saito, K.; Yasumoto, S.; Muranaka, T.; Gharat, S. A.; Kazachkova, Y.; Dong, Y.; Arava, S.; Goliand, I.; Nevo, R.; Rogachev, I.; Meir, S.; Mizutani, M.; Aharoni, A.;A cellulose synthase–like protein governs the biosynthesis of
Solanum
alkaloidsScience386eadq5721(2024)DOI: 10.1126/science.adq5721
Decades of research on the infamous antinutritional steroidal glycoalkaloids (SGAs) in Solanaceae plants have provided deep insights into their metabolism and roles. However, engineering SGAs in heterologous hosts has remained a challenge. We discovered that a protein evolved from the machinery involved in building plant cell walls is the crucial link in the biosynthesis of SGAs. We show that cellulose synthase–like M [GLYCOALKALOID METABOLISM15 (GAME15)] functions both as a cholesterol glucuronosyltransferase and a scaffold protein. Silencing
GAME15
depletes SGAs, which makes plants more vulnerable to pests. Our findings illuminate plant evolutionary adaptations that balance chemical defense and self-toxicity and open possibilities for producing steroidal compounds in heterologous systems for food, cosmetics, and pharmaceuticals.
Publikation
Jaimez, R. E.; Barragan, L.; Fernández-Niño, M.; Larreal B, O. J.; Flores, B.;Pod Production Dynamics and Pod Size Distribution of Theobroma cacao L. Clone CCN 51 in Full SunlightInternational Journal of Agronomy20241-9(2024)DOI: 10.1155/2024/4242270
Cacao fruit production dynamics vary from one location to another and are conditioned by the number of pods produced per tree. During cocoa pod development, the strength of the carbon sink varies depending on the demand exerted by the pods, which is proportional to the size. The relationship between cocoa pod production dynamics and size distribution is still poorly understood. Dissecting this relationship is an important step toward further improving cocoa crop management. In this study, the annual yield dynamics and quantity of cocoa pods produced by popular, highly productive, and widespread clone CCN 51 were investigated, based on six size classes observed during its fructification. Growth parameters were determined as weekly increments of pod length and diameter, whereas daily increments were estimated using the logistic Richards model. The fruiting cycle was characterized by the coexistence of fruits of various sizes where the number of pods belonging to each size class changes throughout the fruiting season. Fruit production varied following a seasonal pattern, reaching a maximum of 36 pods/tree, in trees cultivated in full sunlight, of which approximately 55% matured and were harvested. The peak carbon sink demand occurs when the tree pods have the highest numbers of pods. During this period, 65% of the pods had lengths between 5 and 15 cm, which corresponds to the period of the highest pod growth rate. The average length values of the harvested pods were generally below 23 cm and rarely exceeded 7 pods/tree. The Richard model proved to describe accurately the pod growth rates for CCN 51. This represents a promising tool to determine pod growth in other cultivars of relevance for the cocoa industry, which is essential to improve cocoa crop management.
Publikation
Illig, A.-M.; Siedhoff, N. E.; Davari, M. D.; Schwaneberg, U.;Evolutionary probability and stacked regressions enable data-driven protein engineering with minimized experimental effortJ. Chem. Inf. Model.646350-6360(2024)DOI: 10.1021/acs.jcim.4c00704
Protein engineering through directed evolution and (semi)rational approaches is routinely applied to optimize protein properties for a broad range of applications in industry and academia. The multitude of possible variants, combined with limited screening throughput, hampers efficient protein engineering. Data-driven strategies have emerged as a powerful tool to model the protein fitness landscape that can be explored in silico, significantly accelerating protein engineering campaigns. However, such methods require a certain amount of data, which often cannot be provided, to generate a reliable model of the fitness landscape. Here, we introduce MERGE, a method that combines direct coupling analysis (DCA) and machine learning (ML). MERGE enables data-driven protein engineering when only limited data are available for training, typically ranging from 50 to 500 labeled sequences. Our method demonstrates remarkable performance in predicting a protein’s fitness value and rank based on its sequence across diverse proteins and properties. Notably, MERGE outperforms state-of-the-art methods when only small data sets are available for modeling, requiring fewer computational resources, and proving particularly promising for protein engineers who have access to limited amounts of data.