Disciplinary publications from 2024
'All that glisters is not gold'
NBD-Cl is a fluorescent labeling reagent widely used to track biomolecules such as lipids and proteins or to monitor enzyme activities. However, the potential impact of NBD labeling on cellular metabolism remains a concern. The Optical Nanospectroscopy Group (Janina Kneipp) and the Organic and Bioorganic Chemistry Group (Christoph Arenz) investigated the molecular changes induced by NBD-Cl and NBD-ceramide (NBDCER) in the endolysosomal compartments of 3T3 fibroblast cells and J774 macrophage cells to identify specific molecular alterations and understand their implications for cellular function. Find out more about the 'hidden' contributions of the NBD group in their The Journal of Physical Chemistry C Article!
Abstract
7-Nitrobenz-2-oxa-1,3-diazole (NBD) is a widely used fluorescent label for proteins, peptides, and lipids. Its chloride derivative, NBD-Cl, can be highly reactive toward thiol and amine groups, forming stable fluorescent adducts. When labeling the ubiquitous lipid molecule ceramide, NBD-ceramide (NBDCER) aids in visualizing sphingolipid metabolism in cells. This study investigates intracellular molecular changes induced by NBD-Cl and NBDCER using surface-enhanced Raman scattering (SERS). SERS spectra from the endolysosomal compartment of two cell lines, 3T3 fibroblast cells and J774 macrophage cells, obtained with gold nanoparticles as probes, reveal changes in the molecular composition and interactions under different incubation conditions. Applying the random forest (RF)-based algorithm surrogate minimal depth (SMD) to the SERS data to identify important spectral classifiers and their relations, both NBD-Cl and NBDCER are found to alter the biochemical makeup of the endolysosomal compartment. The data indicate significant structural and interaction changes in the molecular constituents of the cells that are in agreement with possible interference of the labels in the cellular metabolism and the reaction of NBD-Cl with functional groups of cellular molecules.
If I do have a strength, it probably is adaptability...
Plants are able to rapidly adapt to changing environmental conditions. One fundamental adjustment is the expression of chloroplast genes. The essential splicing factor Maturase K has been anticipated to play a generally important role in cholorplast gene regulation, but its importance has so far made it rather difficult to study its function and targets in detail. Together, the Plant Cell and Molecular Biology Group (Kerstin Kaufmann) and the Molecular Genetics Group (Christian Schmitz-Linneweber) investigated which transcripts Maturase K preferably targets and how this translates to a differential expression of functional chloroplast gene groups. Check out their The Plant Journal Article!
Abstract
The protein levels of chloroplast photosynthetic genes and genes related to the chloroplast genetic apparatus vary to adapt to different conditions. However, the underlying mechanisms governing these variations remain unclear. The chloroplast intron Maturase K is encoded within the trnK intron and has been suggested to be required for splicing several group IIA introns, including the trnK intron. In this study, we used RNA immunoprecipitation followed by high-throughput sequencing (RIP-Seq) to identify MatK's preference for binding to group IIA intron domains I and VI within target transcripts. Importantly, these domains are crucial for splice site selection, and we discovered alternative 5′-splice sites in three MatK target introns. The resulting alternative trnK lariat structure showed increased accumulation during heat acclimation. The cognate codon of tRNA-K(UUU) is highly enriched in mRNAs encoding ribosomal proteins and a trnK-matK over-expressor exhibited elevated levels of the spliced tRNA-K(UUU). Ribosome profiling analysis of the overexpressor revealed a significant up-shift in the translation of ribosomal proteins compared to photosynthetic genes. Our findings suggest the existence of a novel regulatory mechanism linked to the abundance of tRNA-K(UUU), enabling the differential expression of functional chloroplast gene groups.
Heart and soul...
Recurrence Quantification Analysis (RQA) is a powerful technique for analyzing the nonlinear dynamics of time series data. However, traditional RQA is limited to univariate time series. To address this limitation, Multidimensional RQA has been developed to analyze the joint dynamics of multivariate time series. The Social and Organizational Psychology Group (Ursula Hess) and the Psychological Assessment Group (Matthias Ziegler) developed a novel extension of Multidimensional RQA, called Lagged Multidimensional RQA, which allows for the investigation of relationships between different variables within a multivariate time series. Find out more about the utilization of Lagged Multidimensional RQA in analyzing joint action research data, specifically focusing on the shared dynamics between facial expressions and heart rate in their Psychological MethodsArticle!
Abstract
The current article introduces lagged multidimensional recurrence quantification analysis. The method is an extension of multidimensional recurrence quantification analysis and allows to quantify the joint dynamics of multivariate time series and to investigate leader–follower relationships in behavioral and physiological data. Moreover, the method enables the quantification of the joint dynamics of a group, when such leader– follower relationships are taken into account. We first provide a formal presentation of the method, and then apply it to synthetic data, as well as data sets from joint action research, investigating the shared dynamics of facial expression and beats-per-minute recordings within different groups. A wrapper function is included, for applying the method together with the “crqa” package in R.