Search results for "formation"
showing 10 items of 21020 documents
The RNA methyltransferase Dnmt2 methylates DNA in the structural context of a tRNA
2016
The amino acid sequence of Dnmt2 is very similar to the catalytic domains of bacterial and eukaryotic DNA-(cytosine 5)-methyltransferases, but it efficiently catalyzes tRNA methylation, while its DNA methyltransferase activity is the subject of controversial reports with rates varying between zero and very weak. By using composite nucleic acid molecules as substrates, we surprisingly found that DNA fragments, when presented as covalent DNA-RNA hybrids in the structural context of a tRNA, can be more efficiently methylated than the corresponding natural tRNA substrate. Furthermore, by stepwise development of tRNAAsp, we showed that this natural Dnmt2 substrate could be engineered to employ R…
Newly Digitized Database Reveals the Lives and Families of Forced Migrants from Finnish Karelia
2017
Studies on displaced persons often suffer from a lack of data on the long-term effects of forced migration. A register created during 1960s and published as a book series ‘Siirtokarjalaisten tie’ in 1970 documented the lives of individuals who fled the southern Karelian district of Finland after its first and second occupation by the Soviet Union in 1940 and 1944. To realize the potential value of these data for scientific research, we have recently scanned the register using optical character recognition (OCR) software, and developed proprietary computer code to extract these data. Here we outline the steps involved in the digitization process, and present an overview of the Migration Kare…
RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures
2017
RepeatsDB 2.0 (URL: http://repeatsdb.bio.unipd.it/) is an update of the database of annotated tandem repeat protein structures. Repeat proteins are a widespread class of non-globular proteins carrying heterogeneous functions involved in several diseases. Here we provide a new version of RepeatsDB with an improved classification schema including high quality annotations for ∼5400 protein structures. RepeatsDB 2.0 features information on start and end positions for the repeat regions and units for all entries. The extensive growth of repeat unit characterization was possible by applying the novel ReUPred annotation method over the entire Protein Data Bank, with data quality is guaranteed by a…
Mechanism and biological role of Dnmt2 in Nucleic Acid Methylation
2016
ABSTRACT A group of homologous nucleic acid modification enzymes called Dnmt2, Trdmt1, Pmt1, DnmA, and Ehmet in different model organisms catalyze the transfer of a methyl group from the cofactor S-adenosyl-methionine (SAM) to the carbon-5 of cytosine residues. Originally considered as DNA MTases, these enzymes were shown to be tRNA methyltransferases about a decade ago. Between the presumed involvement in DNA modification-related epigenetics, and the recent foray into the RNA modification field, significant progress has characterized Dnmt2-related research. Here, we review this progress in its diverse facets including molecular evolution, structural biology, biochemistry, chemical biology,…
Quantitative characterization of translational riboregulators using an in vitro transcription–translation system
2018
Riboregulators are short RNA sequences that, upon binding to a ligand, change their secondary structure and influence the expression rate of a downstream gene. They constitute an attractive alternative to transcription factors for building synthetic gene regulatory networks because they can be engineered de novo. However, riboregulators are generally designed in silico and tested in vivo, which provides little quantitative information about their performances, thus hindering the improvement of design algorithms. Here we show that a cell-free transcription-translation (TX-TL) system provides valuable information about the performances of in silico designed riboregulators. We first propose a …
Cytoplasmic localization of the cell polarity factor scribble supports liver tumor formation and tumor cell invasiveness
2018
The loss of epithelial cell polarity plays an important role in the development and progression of liver cancer. However, the specific molecular mechanisms supporting tumor initiation and progression are poorly understood. In this study, transcriptome data and immunofluorescence stains of tissue samples derived from hepatocellular carcinoma (HCC) patients revealed that overexpression associated with cytoplasmic localization of the baso-lateral cell polarity complex protein Scribble (Scrib) correlated with poor prognosis of HCC patients. In comparison to HCC cells stably expressing wildtype Scrib (ScribWT), mutated Scrib with enforced cytoplasmic enrichment (ScribP305L) induced AKT signaling…
Molecular chaperones in tumors of salivary glands.
2020
The salivary glands are key components of the mouth and play a central role in its physiology. Their importance may be appreciated considering their number, occurrence in pairs, and distribution in the mouth: two parotids, two submandibular, two sublingual, and many other small ones scattered throughout the mouth. They produce saliva, without which ingestion of non-liquid nutrients and speech would be practically impossible. Nevertheless, the physiology and pathology of salivary glands are poorly understood. For instance, tumors of salivary glands occur, and their incidence is on the rise, but their etiology and pathogenesis are virtually unknown, although some risk factors have been identi…
Heat- and pH-induced BSA conformational changes, hydrogel formation and application as 3D cell scaffold
2016
Aggregation and gelation of globular proteins can be an advantage to generate new forms of nanoscale biomaterials based on the fibrillar architecture. Here, we report results obtained by exploiting the proteins' natural tendency to self-organize in 3D network, for the production of new material based on BSA for medical application. In particular, at five different pH values the conformational and structural changes of the BSA during all the steps of the thermal aggregation and gelation have been analyzed by FTIR spectroscopy. The macroscopic mechanical properties of these hydrogels have been obtained by rheological measurements. The microscopic structure of the gels have been studied by AFM…
GSaaS: A Service to Cloudify and Schedule GPUs
2018
Cloud technology is an attractive infrastructure solution that provides customers with an almost unlimited on-demand computational capacity using a pay-per-use approach, and allows data centers to increase their energy and economic savings by adopting a virtualized resource sharing model. However, resources such as graphics processing units (GPUs), have not been fully adapted to this model. Although, general-purpose computing on graphics processing units (GPGPU) is becoming more and more popular, cloud providers lack of flexibility to manage accelerators, because of the extended use of peripheral component interconnect (PCI) passthrough techniques to attach GPUs to virtual machines (VMs). F…
Fragments of peer review: A quantitative analysis of the literature (1969-2015)
2018
This paper examines research on peer review between 1969 and 2015 by looking at records indexed from the Scopus database. Although it is often argued that peer review has been poorly investigated, we found that the number of publications in this field doubled from 2005. A half of this work was indexed as research articles, a third as editorial notes and literature reviews and the rest were book chapters or letters. We identified the most prolific and influential scholars, the most cited publications and the most important journals in the field. Co-authorship network analysis showed that research on peer review is fragmented, with the largest group of co-authors including only 2.1% of the wh…