The comprehensive interactomes of human adenosine RNA methyltransferases and demethylases reveal distinct functional and regulatory features

N6-methyladenosine (m(6)A) and N6,2 '-O-dimethyladenosine (m(6)Am) are two abundant modifications found in mRNAs and ncRNAs that can regulate multiple aspects of RNA biology. They function mainly by regulating interactions with specific RNA-binding proteins. Both modifications are linked to development, disease and stress response. To date, three methyltransferases and two demethylases have been identified that modify adenosines in mammalian mRNAs. Here, we present a comprehensive analysis of the interactomes of these enzymes. PCIF1 protein network comprises mostly factors involved in nascent RNA synthesis by RNA polymerase II, whereas ALKBH5 is closely linked with most aspects of pre-mRNA processing and mRNA export to the cytoplasm. METTL16 resides in subcellular compartments co-inhabited by several other RNA modifiers and processing factors. FTO interactome positions this demethylase at a crossroad between RNA transcription, RNA processing and DNA replication and repair. Altogether, these enzymes share limited spatial interactomes, pointing to specific molecular mechanisms of their regulation.Peer reviewe

Effects of Various Doses of Selenite on Stinging Nettle (Urtica dioica L.)

The aim of this study was to investigate the effects of selenium (Se) on the growth, accumulation and possible mechanisms of Se transport in certain parts (roots, leaves, stamp and apex) of nettle (Urtica dioica L.) plants. Se was supplemented by one-shot and two repeated doses to the soil (2.0 and 4.0 mg Se per kg of substrate). Selenium content in roots increased linearly with dose and was significantly higher compared to other plant parts of interest. However, growth of the above-ground parts of plant as well as roots was slightly inhibited with increasing selenium concentration in comparison to the untreated plants. The content of phytochelatin2, a low molecular mass peptide containing a sulfhydryl group, correlated well with the Se content. This suggests a possible stimulation of synthesis of this plant peptide by Se

Pieces-of-parts for supervoxel segmentation with global context: Application to DCE-MRI tumour delineation

Rectal tumour segmentation in dynamic contrast-enhanced MRI (DCE-MRI) is a challenging task, and an automated and consistent method would be highly desirable to improve the modelling and prediction of patient outcomes from tissue contrast enhancement characteristics – particularly in routine clinical practice. A framework is developed to automate DCE-MRI tumour segmentation, by introducing: perfusion-supervoxels to over-segment and classify DCE-MRI volumes using the dynamic contrast enhancement characteristics; and the pieces-of-parts graphical model, which adds global (anatomic) constraints that further refine the supervoxel components that comprise the tumour. The framework was evaluated on 23 DCE-MRI scans of patients with rectal adenocarcinomas, and achieved a voxelwise area-under the receiver operating characteristic curve (AUC) of 0.97 compared to expert delineations. Creating a binary tumour segmentation, 21 of the 23 cases were segmented correctly with a median Dice similarity coefficient (DSC) of 0.63, which is close to the inter-rater variability of this challenging task. A second study is also included to demonstrate the method’s generalisability and achieved a DSC of 0.71. The framework achieves promising results for the underexplored area of rectal tumour segmentation in DCE-MRI, and the methods have potential to be applied to other DCE-MRI and supervoxel segmentation problems

Sunflower Plants as Bioindicators of Environmental Pollution with Lead (II) Ions

In this study, the influence of lead (II) ions on sunflower growth and biochemistry was investigated from various points of view. Sunflower plants were treated with 0, 10, 50, 100 and/or 500 μM Pb-EDTA for eight days. We observed alterations in growth in all experimental groups compared with non-treated control plants. Further we determined total content of proteins by a Bradford protein assay. By the eighth day of the experiment, total protein contents in all treated plants were much lower compared to control. Particularly noticeable was the loss of approx. 8 μg/mL or 15 μg/mL in shoots or roots of plants treated with 100 mM Pb-EDTA. We also focused our attention on the activity of alanine transaminase (ALT), aspartate transaminase (AST) and urease. Activity of the enzymes increased with increasing length of the treatment and applied concentration of lead (II) ions. This increase corresponds well with a higher metabolic activity of treated plants. Contents of cysteine, reduced glutathione (GSH), oxidized glutathione (GSSG) and phytochelatin 2 (PC2) were determined by high performance liquid chromatography with electrochemical detection. Cysteine content declined in roots of plants with the increasing time of treatment of plants with Pb-EDTA and the concentration of toxic substance. Moreover, we observed ten times higher content of cysteine in roots in comparison with shoots. The observed reduction of cysteine content probably relates with its utilization for biosynthesis of GSH and phytochelatins, because the content of GSH and PC2 was similar in roots and shoots and increased with increased treatment time and concentration of Pb-EDTA. Moreover, we observed oxidative stress caused by Pb-EDTA in roots where the GSSG/GSH ratio was about 0.66. In shoots, the oxidative stress was less distinctive, with a GSSG/GSH ratio 0.14. We also estimated the rate of phytochelatin biosynthesis from the slope of linear equations plotted with data measured in the particular experimental group. The highest rate was detected in roots treated with 100 μM of Pb-EDTA. To determine heavy metal ions many analytical instruments can be used, however, most of them are only able to quantify total content of the metals. This problem can be overcome using laser induced breakdown spectroscopy, because it is able to provide a high spatial-distribution of metal ions in different types of materials, including plant tissues. Data obtained were used to assemble 3D maps of Pb and Mg distribution. Distribution of these elements is concentrated around main vascular bundle of leaf, which means around midrib

Building computational atlases from databases of whole-body clinical PET/CT images

Medical imaging has revolutionized cancer care and its use has grown massively over the past several decades. Images are increasingly stored in large digital image repositories such as hospital Picture Archiving and Communication System, which will hopefully provide a wealth of information on patient conditions and therapy outcomes as cancer diagnosis and therapy moves from 'one size fits all' to more personalized approaches tailored to each particular patient. However, converting the unstructured avalanche of data at thousands of different hospitals into clinically valuable biomarkers and tools requires that the images of different patients can be compared and efficiently searched. Our research aims to develop novel methods to compare whole-body scans of multiple patients; methods which incorporate 'intelligent' prior knowledge of the internal structure of the human body, as opposed to current methods of image registration which mostly rely on matching the voxel intensities and disregard their anatomical meaning. We develop computational methods for accurate and reliable automated localization of anatomical structures in whole-body images, which will help to automate key steps in cancer diagnosis and radiation treatment planning and save expensive clinicians' time while improving the reliability of their decisions. Conventional approaches to determining spatial correspondences between pairs or sets of images in medical imaging typically rely on image registration methods. There have been considerable advances in registration of multiple images of the same patient taken at different time-points, known as longitudinal studies. However, conventional methods, which rely on optimizing certain integral functions of voxel values over the entire image, are unreliable when applied to aligning whole-body images of different patients. Whole-body Computed Tomography (CT) images contain many different anatomical structures whose physical attributes and consequent appearance can be highly variable between patients. This substantial, but normal, variability is further increased by the presence of pathologies such as tumours and non-cancerous diseases, surgical interventions and degenerative changes due to aging as well as different patterns of contrast agent uptake. Conventional registration methods often get trapped in local minima that abound in such images, resulting in unreliable and inaccurate anatomical correspondences. The methods developed in this thesis tackle the problem of inter-patient registration by incorporating prior anatomical knowledge into parts-based graphical models that accurately and reliably localize arbitrary skeletal and soft-tissue anatomical landmarks in whole-body clinical oncology scans. We optimize parts-based graphical models called Pictorial Structures for accurate and reliable landmark localization in CT images and introduce novel methods that replace standard population models by models personalized to the particular patient. We also propose methods that further improve landmark localization while minimizing, as far as possible, the high costs of ground-truth annotation by expert radiologists. We do this by automatically discovering new landmark correspondences from a database of partially annotated images. The performance of the algorithms developed in my thesis is evaluated on a large database of clinical lung cancer PET/CT scans, showing superior accuracy and reliability of landmark localization compared to conventional methods.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Elimination Voltammetry with Linear Scan as a New Detection Method for DNA Sensors

The paper describes successful coupling of adsorptive transfer stripping (AdTS) andelimination voltammetry with linear scan (EVLS) for the resolution of reduction signals of cytosine (C)and adenine (A) residues in hetero-oligodeoxynucleotides (ODNs). Short ODNs (9-mers and 20-mers)were adsorbed from a small volume on a hanging mercury drop electrode (HMDE). After washing ofthe ODN-modified electrode by water and its transferring to an electrochemical cell, voltammetric curves were measured. The AdTS EVLS was able to determine of C/A ratio of ODNs through theelimination function conserving the diffusion current component and eliminating kinetic and chargingcurrent components. This function, which provides the elimination signal in a peak-counterpeak form,increased the current sensitivity for A and C resolution, and for the recognition of bases sequences inODN chains. Optimal conditions of elimination experiments such as pH, time of adsorption, and scanrate were found. The combination of EVLS with AdTS procedure can be considered as a newdetection method in a DNA sensor