Structure of plasma (re)polymerized polylactic acid films fabricated by plasma-assisted vapour thermal deposition

Plasma polymer films typically consist of very short fragments of the precursor molecules. That rather limits the applicability of most plasma polymerisation/plasma-enhanced chemical vapour deposition (PECVD) processes in cases where retention of longer molecular structures is desirable. Plasma-assisted vapour thermal deposition (PAVTD) circumvents this limitation by using a classical bulk polymer as a high molecular weight “precursor”. As a model polymer in this study, polylactic acid (PLA) has been used. The resulting PLA-like films were characterised mostly by X-ray photoelectron spectroscopy (XPS) and nuclear magnetic resonance (NMR) spectroscopy. The molecular structure of the films was found to be tunable in a broad range: from the structures very similar to bulk PLA polymer to structures that are more typical for films prepared using PECVD. In all cases, PLA-like groups are at least partially preserved. A simplified model of the PAVTD process chemistry was proposed and found to describe well the observed composition of the films. The structure of the PLA-like films demonstrates the ability of plasma-assisted vapour thermal deposition to bridge the typical gap between the classical and plasma polymers. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.Czech Science FoundationGrant Agency of the Czech Republic [GA17-10813S]; Charles University [SVV 260 579-2020]Univerzita Karlova v Praze, UK; Grantová Agentura České Republiky, GA ČR: GA17-10813

Plasma polymers as targets for laser-driven proton-boron fusion

Laser-driven proton-boron (pB) fusion has been gaining significant interest for energetic alpha particles production because of its neutron-less nature. This approach requires the use of B- and H-rich materials as targets, and common practice is the use of BN and conventional polymers. In this work, we chose plasma-assisted vapour phase deposition to prepare films of oligoethylenes (plasma polymers) on Boron Nitride BN substrates as an advanced alternative. The r.f. power delivered to the plasma was varied between 0 and 50 W to produce coatings with different crosslink density and hydrogen content, while maintaining the constant thickness of 1 μm. The chemical composition, including the hydrogen concentration, was investigated using XPS and RBS/ERDA, whereas the surface topography was analyzed using SEM and AFM. We triggered the pB nuclear fusion reaction focusing laser pulses from two different systems (i.e., the TARANIS multi-TW laser at the Queen’s University Belfast (United Kingdom) and the PERLA B 10-GW laser system at the HiLASE center in Prague (Czech Republic)) directly onto these targets. We achieved a yield up to 108 and 104 alpha particles/sr using the TARANIS and PERLA B lasers, respectively. Radiative-hydrodynamic and particle-in-cell PIC simulations were performed to understand the laser-target interaction and retrieve the energy spectra of the protons. The nuclear collisional algorithm implemented in the WarpX PIC code was used to identify the region where pB fusion occurs. Taken together, the results suggest a complex relationship between the hydrogen content, target morphology, and structure of the plasma polymer, which play a crucial role in laser absorption, target expansion, proton acceleration and ultimately nuclear fusion reactions in the plasma

Structuring of plasma polymers: new methods for fabrication of nano-architectured thin films

Title: Structuring of plasma polymers: new methods for fabrication of nano-architectured thin films Author: Daniil Nikitin Department / Institute: Department of Macromolecular Physics/Charles University Supervisor of the doctoral thesis: Doc. Ing. Andrey Shukurov, PhD, Department of Macromolecular Physics/Charles University Abstract: The PhD thesis aims at the investigation of nanostructures based on plasma polymers. The main attention is paid to the combination of a gas aggregation cluster source with plasma-assisted vapor phase deposition for the fabrication of metal-polymer nanocomposites with bactericidal potential. Copper nanoparticles were incorporated into a biocompatible matrix of plasma polymerized poly(ethylene oxide) (ppPEO). The efficiency of such nanocomposite against multi-drug resistant bacteria was demonstrated. It was found that the segmental dynamics of the plasma polymer significantly changed in the presence of nanoparticles as revealed by the measurements of the dynamic glass transition temperature. The nanoscale confinement crucially influences the non-fouling properties of poly(ethylene oxide). A separate chapter is dedicated to the examination of the nanoparticle formation, growth and transport inside the source. Copper and silver nanoparticles were detected in situ in the gas phase..

Structuring of plasma polymers: new methods for fabrication of nano-architectured thin films

Title: Structuring of plasma polymers: new methods for fabrication of nano-architectured thin films Author: Daniil Nikitin Department / Institute: Department of Macromolecular Physics/Charles University Supervisor of the doctoral thesis: Doc. Ing. Andrey Shukurov, PhD, Department of Macromolecular Physics/Charles University Abstract: The PhD thesis aims at the investigation of nanostructures based on plasma polymers. The main attention is paid to the combination of a gas aggregation cluster source with plasma-assisted vapor phase deposition for the fabrication of metal-polymer nanocomposites with bactericidal potential. Copper nanoparticles were incorporated into a biocompatible matrix of plasma polymerized poly(ethylene oxide) (ppPEO). The efficiency of such nanocomposite against multi-drug resistant bacteria was demonstrated. It was found that the segmental dynamics of the plasma polymer significantly changed in the presence of nanoparticles as revealed by the measurements of the dynamic glass transition temperature. The nanoscale confinement crucially influences the non-fouling properties of poly(ethylene oxide). A separate chapter is dedicated to the examination of the nanoparticle formation, growth and transport inside the source. Copper and silver nanoparticles were detected in situ in the gas phase..

Strukturování plazmových polymerů: nové metody přípravy tenkých vrstev s nano-architekturou

Název práce: Strukturování plazmových polymerů: nové metody přípravy tenkých vrstev s nano-architekturou Autor: Daniil Nikitin Katedra/Ústav: Katedra Makromolekulární Fyziky/Univerzita Karlova Vedoucí doktorské práce: Doc. Ing. Andrey Shukurov, PhD Abstrakt: Disertační práce je zaměřena na studium nanostruktur na bázi plazmových polymerů. Hlavní pozornost je věnována přípravě antibakteriálních nanokompozitních vrstev kov/polymer za použití plynového agregačního zdroje nanočástic a plazmatem asistované depozice z plynné fáze. Do biokompatibilní matrice plazmového polymeru poly(ethylen oxidu) (ppPEO) byly začleněny měděné nanočástice. Byla prokázána účinnost těchto nanokompozitů proti multi-rezistentním bakteriím. Pomocí měření dynamické teploty skelného přechodu bylo zjištěno, že se v přítomnosti nanočástic významně změnila segmentová dynamika plazmového polymeru. To zásadně ovlivnilo bio-rezistentní vlastnosti poly(ethylen oxidu). Samostatná kapitola je věnována studiu vzniku, růstu a transportu nanočástic uvnitř zdroje. Měděné a stříbrné nanočástice byly detekovány in situ v plynné fázi buďto pomocí maloúhlového rozptylu rentgenového záření, nebo pomocí UV-Vis spektroskopie. Vůbec poprvé bylo zjištěno zachytávání kovových nanočástic v plazmatu. Navíc byla potvrzena částečná re-depozice nanočástic na terč a...Title: Structuring of plasma polymers: new methods for fabrication of nano-architectured thin films Author: Daniil Nikitin Department / Institute: Department of Macromolecular Physics/Charles University Supervisor of the doctoral thesis: Doc. Ing. Andrey Shukurov, PhD, Department of Macromolecular Physics/Charles University Abstract: The PhD thesis aims at the investigation of nanostructures based on plasma polymers. The main attention is paid to the combination of a gas aggregation cluster source with plasma-assisted vapor phase deposition for the fabrication of metal-polymer nanocomposites with bactericidal potential. Copper nanoparticles were incorporated into a biocompatible matrix of plasma polymerized poly(ethylene oxide) (ppPEO). The efficiency of such nanocomposite against multi-drug resistant bacteria was demonstrated. It was found that the segmental dynamics of the plasma polymer significantly changed in the presence of nanoparticles as revealed by the measurements of the dynamic glass transition temperature. The nanoscale confinement crucially influences the non-fouling properties of poly(ethylene oxide). A separate chapter is dedicated to the examination of the nanoparticle formation, growth and transport inside the source. Copper and silver nanoparticles were detected in situ in the gas phase...Katedra makromolekulární fyzikyDepartment of Macromolecular PhysicsMatematicko-fyzikální fakultaFaculty of Mathematics and Physic

Profiling of Human Molecular Pathways Affected by Retrotransposons at the Level of Regulation by Transcription Factor Proteins

Endogenous retroviruses and retrotransposons also termed retroelements (REs) are mobile genetic elements that were active until recently in human genome evolution. REs regulate gene expression by actively reshaping chromatin structure or by directly providing transcription factor binding sites (TFBSs). We aimed to identify molecular processes most deeply impacted by the REs in human cells at the level of TFBS regulation. By using ENCODE data, we identified ~2 million TFBS overlapping with putatively regulation-competent human REs located in 5-kb gene promoter neighborhood (~17% of all TFBS in promoter neighborhoods; ~9% of all RE-linked TFBS). Most of REs hosting TFBS were highly diverged repeats, and for the evolutionary young (0–8% diverged) elements we identified only ~7% of all RE-linked TFBS. The gene-specific distributions of RE-linked TFBS generally correlated with the distributions for all TFBS. However, several groups of molecular processes were highly enriched in the RE-linked TFBS regulation. They were strongly connected with the immunity and response to pathogens, with the negative regulation of gene transcription, ubiquitination, and protein degradation, extracellular matrix organization, regulation of STAT signaling, fatty acids metabolism, regulation of GTPase activity, protein targeting to Golgi, regulation of cell division and differentiation, development and functioning of perception organs and reproductive system. By contrast, the processes most weakly affected by the REs were linked with the conservative aspects of embryo development. We also identified differences in the regulation features by the younger and older fractions of the REs. The regulation by the older fraction of the REs was linked mainly with the immunity, cell adhesion, cAMP, IGF1R, Notch, Wnt, and integrin signaling, neuronal development, chondroitin sulfate and heparin metabolism, and endocytosis. The younger REs regulate other aspects of immunity, cell cycle progression and apoptosis, PDGF, TGF beta, EGFR, and p38 signaling, transcriptional repression, structure of nuclear lumen, catabolism of phospholipids, and heterocyclic molecules, insulin and AMPK signaling, retrograde Golgi-ER transport, and estrogen signaling. The immunity-linked pathways were highly represented in both categories, but their functional roles were different and did not overlap. Our results point to the most quickly evolving molecular pathways in the recent and ancient evolution of human genome

High FREM2 gene and protein expression are associated with favorable prognosis of IDH-WT glioblastomas

World Health Organization grade IV diffuse gliomas, known as glioblastomas, are the most common malignant brain tumors, and they show poor prognosis. Multimodal treatment of surgery followed by radiation and chemotherapy is not sufficient to increase patient survival, which is 12 to 18 months after diagnosis. Despite extensive research, patient life expectancy has not significantly improved over the last decade. Previously, we identified FREM2 and SPRY1 as genes with differential expression in glioblastoma cell lines compared to nonmalignant astrocytes. In addition, the FREM2 and SPRY1 proteins show specific localization on the surface of glioblastoma cells. In this study, we explored the roles of the FREM2 and SPRY1 genes and their proteins in glioblastoma pathology using human tissue samples. We used proteomic, transcriptomic, and bioinformatics approaches to detect changes at different molecular levels. We demonstrate increased FREM2 protein expression levels in glioblastomas compared to reference samples. At the transcriptomic level, both FREM2 and SPRY1 show increased expression in tissue samples of different glioma grades compared to nonmalignant brain tissue. To broaden our experimental findings, we analyzed The Cancer Genome Atlas glioblastoma patient datasets. We discovered higher FREM2 and SPRY1 gene expression levels in glioblastomas compared to lower grade gliomas and reference samples. In addition, we observed that low FREM2 expression was associated with progression of IDH-mutant low-grade glioma patients. Multivariate analysis showed positive association between FREM2 and favorable prognosis of IDH-wild type glioblastoma. We conclude that FREM2 has an important role in malignant progression of glioblastoma, and we suggest deeper analysis to determine its involvement in glioblastoma pathology

Retroelement-Linked H3K4me1 Histone Tags Uncover Regulatory Evolution Trends of Gene Enhancers and Feature Quickly Evolving Molecular Processes in Human Physiology

Background: Retroelements (REs) are mobile genetic elements comprising ~40% of human DNA. They can reshape expression patterns of nearby genes by providing various regulatory sequences. The proportion of regulatory sequences held by REs can serve a measure of regulatory evolution rate of the respective genes and molecular pathways. Methods: We calculated RE-linked enrichment scores for individual genes and molecular pathways based on ENCODE project epigenome data for enhancer-specific histone modification H3K4me1 in five human cell lines. We identified consensus groups of molecular processes that are enriched and deficient in RE-linked H3K4me1 regulation. Results: We calculated H3K4me1 RE-linked enrichment scores for 24,070 human genes and 3095 molecular pathways. We ranked genes and pathways and identified those statistically significantly enriched and deficient in H3K4me1 RE-linked regulation. Conclusion: Non-coding RNA genes were statistically significantly enriched by RE-linked H3K4me1 regulatory modules, thus suggesting their high regulatory evolution rate. The processes of gene silencing by small RNAs, DNA metabolism/chromatin structure, sensory perception/neurotransmission and lipids metabolism showed signs of the fastest regulatory evolution, while the slowest processes were connected with immunity, protein ubiquitination/degradation, cell adhesion, migration and interaction, metals metabolism/ion transport, cell death, intracellular signaling pathways

Retroelement—Linked Transcription Factor Binding Patterns Point to Quickly Developing Molecular Pathways in Human Evolution

Background: Retroelements (REs) are transposable elements occupying ~40% of the human genome that can regulate genes by providing transcription factor binding sites (TFBS). RE-linked TFBS profile can serve as a marker of gene transcriptional regulation evolution. This approach allows for interrogating the regulatory evolution of organisms with RE-rich genomes. We aimed to characterize the evolution of transcriptional regulation for human genes and molecular pathways using RE-linked TFBS accumulation as a metric. Methods: We characterized human genes and molecular pathways either enriched or deficient in RE-linked TFBS regulation. We used ENCODE database with mapped TFBS for 563 transcription factors in 13 human cell lines. For 24,389 genes and 3124 molecular pathways, we calculated the score of RE-linked TFBS regulation reflecting the regulatory evolution rate at the level of individual genes and molecular pathways. Results: The major groups enriched by RE regulation deal with gene regulation by microRNAs, olfaction, color vision, fertilization, cellular immune response, and amino acids and fatty acids metabolism and detoxication. The deficient groups were involved in translation, RNA transcription and processing, chromatin organization, and molecular signaling. Conclusion: We identified genes and molecular processes that have characteristics of especially high or low evolutionary rates at the level of RE-linked TFBS regulation in human lineage