SVD-clustering, a general image-analyzing method explained and demonstrated on model and Raman micro-spectroscopic maps

An image analyzing method (SVD-clustering) is presented. Amplitude vectors of SVD factorization (V1…Vi) were introduced into the imaging of the distribution of the corresponding Ui basis-spectra. Since each Vi vector contains each point of the map, plotting them along the X, Y, Z dimensions of the map reconstructs the spatial distribution of the corresponding Ui basis-spectrum. This gives valuable information about the first, second, etc. higher-order deviations present in the map. We extended SVD with a clustering method, using the significant Vi vectors from the VT matrix as coordinates of image points in a ne-dimensional space (ne is the effective rank of the data matrix). This way every image point had a corresponding coordinate in the ne-dimensional space and formed a point set. Clustering was applied to this point set. SVD-clustering is universal; it is applicable to any measurement where data are recorded as a function of an external parameter (time, space, temperature, concentration, species, etc.). Consequently, our method is not restricted to spectral imaging, it can find application in many different 2D and 3D image analyses. Using SVD-clustering, we have shown on models the theoretical possibilities and limitations of the method, especially in the context of creating, meaning/interpreting of cluster spectra. Then for real-world samples, two examples are presented, where we were able to reveal minute alterations in the samples (changing cation ratios in minerals, differently structured cellulose domains in plant root) with spatial resolution. © 2020, The Author(s)

A foszfatidilglicerol szerepe fotoszintetikus membránok szerkezetének kialakításában = The essential role of phosphatidylglycerol in the formation of photosynthetic membrane structure

A negatív töltéssel rendelkező lipidek közül a foszfatidilglicerol (PG) jelentős szerepet tölt be. 1. Létrehoztuk egy FG szintézisben gátolt Synechocytis PCC6803 mutánst melyben megnéztük a CP43 kapcsolódását a kettes fotokémiai rendszer reakció centrumához. Ezt a mutánst egy, a fénybegyűjtő rendszer nélküli mutánssal hoztuk létre, a cdsA gén inaktiválásával. Megállapítottuk, hogy az FG kiürülés hatására a CP43 fehérje bekötődése gátolt. Megállapítottuk, hogy az FG kiürülés csökkenti a cianobaktérium sejtek oxigénfejlesztő képességét. 2. Megállapítottuk, hogy az FG kiürülés megváltoztatja a fotoszintetikus membrán felszíni töltését. 3. Az FG molekulák hatására bekövetkező fotoszintetikus aktivitást a reakció centrumok megváltozása okozza. A reakció centrumok fényérzékennyé vállnak. Ez ellen a sejtek megnövekedett karotin tartalommal védekeznek. A myxoxantin és az echinenon mennyisége nő meg. 4. A Syenechococcus PCC PCC7942 cdsA mutáns létrehozásával igazoltuk, hogy az FG molekulák szerepe a fotoszintetikus szervezetekben általánosítható. Megállapítottuk, hogy az FG kiürülés a különböző törzseken különböző mértékben hat. 5 Az FG molekulák kiürülésének hatására bekövetkező stressz elleni protekció a karotinoid molekulák megjelenése fotoszintetikus reakció centrumokbanmellett megfigyeltük azt is, hogy az FG molekulák zsírsav összetétele megváltozik. A molekulák átalakulását tömegspektometriásan igazoltuk. Az eredményeinket egy áttekintő cikkünkben foglaltuk össze. | Among the negatively charged lipids phosphatidylglycerol (PG) plays an important role. We used transformable cyanobacterial strains.1n We used a Phycobilisome-less mutant of Synechocytis PCC6803 was transformed with inactivated cdsA and the synthesis of PG was blocked. Binding of CP43 to the reaction center complex was investigated. The oxygen evolving activity of mutant was reduced. 2. The PG-depletion affected the surface charge of membranes. 3. PG-depletion induced sensitivity of cells which was compensated by elevated carotenoid content, mainly myxoxanthophyll and echinenone. 4. We generated Syenechococcus PCC PCC7942 cdsA mutant with which we could generalize the importance of PG in photosynthetic organizms. However, we could observe slight differencein different mutant. 5. Westudied PG remodeling by mas spectrometry

The late steps of plant nonsense-mediated mRNA decay

Nonsense-mediated mRNA decay (NMD) is a eukaryotic quality control system that identifies and degrades mRNAs containing premature termination codons (PTCs). If translation terminates at a PTC, the UPF1 NMD factor binds the terminating ribosome and recruits UPF2 and UPF3 to form a functional NMD complex, which triggers the rapid decay of the PTC-containing transcript. Although NMD deficiency is seedling lethal in plants, the mechanism of plant NMD remains poorly understood. To understand how the formation of the NMD complex leads to transcript decay we functionally mapped the UPF1 and SMG7 plant NMD factors, the putative key players of NMD target degradation. Our data indicate that the cysteine–histidine-rich (CH) and helicase domains of UPF1 are only essential for the early steps of NMD, whereas the heavily phosphorylated N- and C–terminal regions play a redundant but essential role in the target transcript degradation steps of NMD. We also show that both the N- and the C–terminal regions of SMG7 are essential for NMD. The N terminus contains a phosphoserine-binding domain that is required for the early steps of NMD, whereas the C terminus is required to trigger the degradation of NMD target transcripts. Moreover, SMG7 is a P–body component that can also remobilize UPF1 from the cytoplasm into processing bodies (P bodies). We propose that the N- and C–terminal phosphorylated regions of UPF1 recruit SMG7 to the functional NMD complex, and then SMG7 transports the PTC-containing transcripts into P bodies for degradation