Dystrophin deficiency affects human astrocyte properties and response to damage.

In addition to progressive muscular degeneration due to dystrophin mutations, 1/3 of Duchenne muscular dystrophy (DMD) patients present cognitive deficits. However, there is currently an incomplete understanding about the function of the multiple dystrophin isoforms in human brains. Here, we tested the hypothesis that dystrophin deficiency affects glial function in DMD and could therefore contribute to neural impairment. We investigated human dystrophin isoform expression with development and differentiation and response to damage in human astrocytes from control and induced pluripotent stem cells from DMD patients. In control cells, short dystrophin isoforms were up-regulated with development and their expression levels changed differently upon neuronal and astrocytic differentiation, as well as in 2-dimensional versus 3-dimensional astrocyte cultures. All DMD-astrocytes tested displayed altered morphology, proliferative activity and AQP4 expression. Furthermore, they did not show any morphological change in response to inflammatory stimuli and their number was significantly lower as compared to stimulated healthy astrocytes. Finally, DMD-astrocytes appeared to be more sensitive than controls to oxidative damage as shown by their increased cell death. Behavioral and metabolic defects in DMD-astrocytes were consistent with gene pathway dysregulation shared by lines with different mutations as demonstrated by bulk RNA-seq analysis. Together, our DMD model provides evidence for altered astrocyte function in DMD suggesting that defective astrocyte responses may contribute to neural impairment and might provide additional potential therapeutic targets.

Microarray analysis of LTR retrotransposon silencing identifies Hdac1 as a regulator of retrotransposon expression in mouse embryonic stem cells.

Retrotransposons are highly prevalent in mammalian genomes due to their ability to amplify in pluripotent cells or developing germ cells. Host mechanisms that silence retrotransposons in germ cells and pluripotent cells are important for limiting the accumulation of the repetitive elements in the genome during evolution. However, although silencing of selected individual retrotransposons can be relatively well-studied, many mammalian retrotransposons are seldom analysed and their silencing in germ cells, pluripotent cells or somatic cells remains poorly understood. Here we show, and experimentally verify, that cryptic repetitive element probes present in Illumina and Affymetrix gene expression microarray platforms can accurately and sensitively monitor repetitive element expression data. This computational approach to genome-wide retrotransposon expression has allowed us to identify the histone deacetylase Hdac1 as a component of the retrotransposon silencing machinery in mouse embryonic stem cells, and to determine the retrotransposon targets of Hdac1 in these cells. We also identify retrotransposons that are targets of other retrotransposon silencing mechanisms such as DNA methylation, Eset-mediated histone modification, and Ring1B/Eed-containing polycomb repressive complexes in mouse embryonic stem cells. Furthermore, our computational analysis of retrotransposon silencing suggests that multiple silencing mechanisms are independently targeted to retrotransposons in embryonic stem cells, that different genomic copies of the same retrotransposon can be differentially sensitive to these silencing mechanisms, and helps define retrotransposon sequence elements that are targeted by silencing machineries. Thus repeat annotation of gene expression microarray data suggests that a complex interplay between silencing mechanisms represses retrotransposon loci in germ cells and embryonic stem cells.

Exploratory Data Analysis for the Evaluation of Tribological Properties of Wear-Resistant Surface Layers Modified with Rare-Earth Metals.

The role of rare Earth metals in the improvement of the properties of metals and alloys has been analysed and described in multiple studies. Their effects on changes in microstructure and mechanical properties are most pronounced. This paper focuses on the beneficial effect of rare Earth metal oxides on the wear resistance of surface layers applied to castings intended for structural elements of machinery and equipment in mining and recycling. The experiment involved modifying prepared surfaces by adding CeO2, Y2O3, and La2O3. Hardness measurements, a scratch test, and tribological tests were performed under dry and fluid friction. The maximum wear track depth and track area were measured from the surface profile. To determine correlations between the results, exploratory data analysis was employed. Heatmaps were used to illustrate strong positive and negative interactions. The addition of oxides at increasing carbon content resulted in increased hardness, lower coefficient of friction, and reduced track area and maximum track depth. Strong negative interactions between the track area and maximum track depth were found. The differences resulting from the test conditions (fluid and dry friction) were discussed. This study demonstrated the suitability of exploratory data analysis for analysing research results and confirmed the improvement of modified surface wear resistance.

Assessment of the Functional Properties of 316L Steel Alloy Subjected to Ion Implantation Used in Biotribological Systems.

Clinical trials conducted in many centres worldwide indicate that, despite advances made in the use of biomaterials for medical applications, tribocorrosive wear remains a significant issue. The release of wear residue into body fluids can cause inflammation and, as a result, implant failure. Surface modification is one of the methods used to improve the mechanical, tribological, and fatigue properties of biomaterials. In this article, the authors investigated the impact of ion implantation on improving the functional properties of implant surfaces. This paper presents morphology, geometric surface structure, hardness, and tribological test results for layers obtained by ion implantation with nitrogen and oxygen ions on alloy 316L. The surface morphology and thickness of the implanted layer were examined using scanning microscopy. Atomic force microscopy was used to evaluate the geometric structure of the surface. Instrumented indentation was used to measure nanohardness. Model tribo tests were carried out for reciprocating motion under conditions of dry friction and lubricated friction with Ringer's solution. The tribological tests showed that the implanted samples had a lower wear than the reference samples. Nitrogen ion implantation increased the hardness of 316L steel by about 45% and increased it by about 15% when oxygen ions were used.

Tribochemical Interactions between Graphene and ZDDP in Friction Tests for Uncoated and W-DLC-Coated HS6-5-2C Steel.

If a lubricant contains structures capable of conducting energy, reactions involving zinc dialkyldithiophosphate (ZDDP) may take place both very close to and away from the solid surfaces, with this indicating that ZDDP can be a highly effective anti-wear (AW) additive. The central thesis of this article is that the tribocatalytic effect is observed only when the energy emitted by the solids is transmitted by ordered molecular structures present in the lubricant, e.g., graphene. The friction tests were carried out for 100Cr6 steel balls in a sliding contact with uncoated or W-DLC-coated HS6-5-2C steel discs in the presence of polyalphaolefin 8 (PAO 8) as the lubricant, which was enhanced with graphene and/or ZDDP. There is sufficient evidence of the interactions occurring between ZDDP and graphene and their effects on the tribological performance of the system. It was also found that the higher the concentration of zinc in the wear area, the lower the wear. This was probably due to the energy transfer resulting from the catalytic decomposition of ZDDP molecules. Graphene, playing the role of the catalyst, contributed to that energy transfer.

Tribochemical Interactions between Carbon Nanotubes and ZDDP Antiwear Additive during Tribofilm Formation on Uncoated and DLC-Coated Steel.

The data from the authors' earlier investigations show that molecules of zinc dithiophosphate (ZDDP) added to a lubricant can absorb energy emitted by a solid surface, which is where triboreactions occur. If the lubricant contains structures able to conduct energy, the ZDDP reactions can occur even at a relatively large distance from the solid surface, which should increase the effectiveness of ZDDP as an antiwear additive. The purpose of this paper was to verify the thesis that the tribocatalytic effect depends on the ability of the solid surface to emit electrons/energy and the ability of ordered molecular structures, such as carbon nanotubes (CNTs), to conduct energy and, most likely, to enhance the energy transfer. The tribological tests were performed using a TRB3 tribotester for 100Cr6 steel balls and uncoated or a-C:H coated HS6-5-2C steel discs. Polyalphaolefin 8 (PAO8) and PAO8 mixed with ZDDP and CNTs were used as lubricants. The results of the tribological tests suggested that: (a) the effect of the interactions between ZDDP and CNTs was clearly visible; (b) the structure and properties of the solid surface layer had a significant influence on the antiwear action of the ZDDP additive.

Small ncRNA transcriptome analysis from kinetoplast mitochondria of Leishmania tarentolae.

Gene expression in mitochondria of kinetoplastid protozoa requires RNA editing, a post-transcriptional process which involves insertion or deletion of uridine residues at specific sites within mitochondrial pre-mRNAs. Sequence specificity of the RNA editing process is mediated by oligo-uridylated small, non-coding RNAs, designated as guide RNAs (gRNAs). In this study, we have analyzed the small ncRNA transcriptome from kinetoplast mitochondria of Leishmania tarentolae by generating specialized cDNA libraries encoding size-selected RNA species. Through this screen, a significant number of novel oligo-uridylated RNA species, which we have termed oU-RNAs, has been identified. Most novel oU-RNAs are present as stable RNA species in mitochondria as assessed by northern blot analysis. Thereby, novel oU-RNAs show similar expression levels and sizes as previously reported for canonical gRNAs. Several oU-RNAs are transcribed from both strands of the maxicircle and minicircles components of the mitochondrial genome, from regions where up till now no transcription has been reported. Two stable oU-RNAs exhibit an anchor sequence in antisense orientation to known gRNAs and thus might regulate editing of respective pre-mRNAs. A number of oU-RNAs map in antisense orientation to non-edited protein-coding genes suggesting that they might function by a different mechanism. In addition, our screen shows that all kinetoplast-derived RNAs are prone to some degree of uridylation.

Identification of novel guide RNAs from the mitochondria of Trypanosoma brucei.

The majority of mitochondrial mRNAs in African trypanosomes are subject to an RNA editing reaction, which is characterized by the insertion and/or deletion of U nucleotides only. The reaction creates functional mRNAs and is catalyzed by a high molecular mass enzyme complex, the editosome. Editosomes interact with a unique class of small non-coding, 3'-oligouridylated (oU) RNAs, so-called guide RNAs (gRNAs). Guide RNAs function as transacting templates in the U deletion/insertion reaction and thus, represent key components in the reaction cycle. Furthermore, by utilizing different gRNAs, alternative editing events can take place, thereby expanding the protein diversity in the mitochondria of the parasites. In this study, we have analyzed small, non-coding mitochondrial transcripts from Trypanosoma brucei. By generating cDNA libraries from size-selected RNA populations we identified 51 novel oU-RNAs. For 29 of these RNAs we were able to predict cognate mRNA targets. By Northern blot analysis, we verified the expression of 22 of these oU-RNAs and demonstrate that they share all known gRNA characteristics. Five of these 51 putative gRNAs are characterized by single mismatches to their cognate, fully edited mRNA sequences suggesting that they could act as gRNAs for alternative editing events.

Identification of small non-coding RNAs from mitochondria and chloroplasts.

Small non-protein-coding RNAs (ncRNAs) have been identified in a wide spectrum of organisms ranging from bacteria to humans. In eukarya, systematic searches for ncRNAs have so far been restricted to the nuclear or cytosolic compartments of cells. Whether or not small stable non-coding RNA species also exist in cell organelles, in addition to tRNAs or ribosomal RNAs, is unknown. We have thus generated cDNA libraries from size-selected mammalian mitochondrial RNA and plant chloroplast RNA and searched for small ncRNA species in these two types of DNA-containing cell organelles. In total, we have identified 18 novel candidates for organellar ncRNAs in these two cellular compartments and confirmed expression of six of them by northern blot analysis or RNase A protection assays. Most candidate ncRNA genes map to intergenic regions of the organellar genomes. As found previously in bacteria, the presumptive ancestors of present-day chloroplasts and mitochondria, we also observed examples of antisense ncRNAs that potentially could target organelle-encoded mRNAs. The structural features of the identified ncRNAs as well as their possible cellular functions are discussed. The absence from our libraries of abundant small RNA species that are not encoded by the organellar genomes suggests that the import of RNAs into cell organelles is of very limited significance or does not occur at all.

Apoptosis and DNA methylation.

Epigenetic mechanisms assist in maintaining gene expression patterns and cellular properties in developing and adult tissues. The molecular pathology of disease states frequently includes perturbation of DNA and histone methylation patterns, which can activate apoptotic pathways associated with maintenance of genome integrity. This perspective focuses on the pathways linking DNA methyltransferases and methyl-CpG binding proteins to apoptosis, and includes new bioinformatic analyses to characterize the evolutionary origin of two G/T mismatch-specific thymine DNA glycosylases, MBD4 and TDG.

The interaction of xKaiso with xTcf3: a revised model for integration of epigenetic and Wnt signalling pathways.

We demonstrate that a direct interaction between the methyl-CpG-dependent transcription repressor Kaiso and xTcf3, a transducer of the Wnt signalling pathway, results in their mutual disengagement from their respective DNA-binding sites. Thus, the transcription functions of xTcf3 can be inhibited by overexpression of Kaiso in cell lines and Xenopus embryos. The interaction of Kaiso with xTcf3 is highly conserved and is dependent on its zinc-finger domains (ZF1-3) and the corresponding HMG DNA-binding domain of TCF3/4 factors. Our data rule out a model suggesting that xKaiso is a direct repressor of Wnt signalling target genes in early Xenopus development via binding to promoter-proximal CTGCNA sequences as part of a xTcf3 repressor complex. Instead, we propose that mutual inhibition by Kaiso/TCF3 of their DNA-binding functions may be important in developmental or cancer contexts and acts as a regulatory node that integrates epigenetic and Wnt signalling pathways.

The non-methylated DNA-binding function of Kaiso is not required in early Xenopus laevis development.

Mammalian forms of the transcription repressor, Kaiso, can reportedly bind methylated DNA and non-methylated CTGCNA motifs. Here we compare the DNA-binding properties of Kaiso from frog, fish and chicken and demonstrate that only the methyl-CpG-binding function of Kaiso is evolutionarily conserved. We present several independent experimental lines of evidence that the phenotypic abnormalities associated with xKaiso-depleted Xenopus laevis embryos are independent of the putative CTGCNA-dependent DNA-binding function of xKaiso. Our analysis suggests that xKaiso does not play a role in the regulation of either xWnt11 or Siamois, key signalling molecules in the Wnt pathway during X. laevis gastrulation. The major phenotypic defects associated with xKaiso depletion are premature transcription activation before the mid-blastula transition and concomitant activation of a p53-dependent cell-death pathway.

Detection of small RNAs in Pseudomonas aeruginosa by RNomics and structure-based bioinformatic tools.

Inactivation of the Pseudomonas aeruginosa (PAO1) hfq gene, encoding the Sm-like Hfq protein, resulted in pleiotropic effects that included an attenuated virulence. As regulation by Hfq often involves the action of small regulatory RNAs (sRNAs), we have used a shotgun cloning approach (RNomics) and bioinformatic tools to identify sRNAs in strain PAO1. For cDNA library construction, total RNA was extracted from PAO1 cultures either grown to stationary phase or exposed to human serum. The cDNA libraries were generated from small-sized RNAs of PAO1 after co-immunoprecipitation with Hfq. Of 400 sequenced cDNA clones, 11 mapped to intergenic regions. Band-shift assays and Northern blot analyses performed with two selected sRNAs confirmed that Hfq binds to and affects the steady-state levels of these RNAs. A proteome study performed upon overproduction of one sRNA, PhrS, implicated it in riboregulation. PhrS contains an ORF, and evidence for its translation is presented. In addition, based on surveys with structure-based bioinformatic tools, we provide an electronic compilation of putative sRNA and non-coding RNA genes of PAO1 based on their evolutionarily conserved structure.