DFT study of water on graphene: Synergistic effect of multilayer p-doping.

Recent experiments related to a study concerning the adsorption of water on graphene have demonstrated the p-doping of graphene, although most of the ab initio calculations predict nearly zero doping. To shed more light on this problem, we have carried out van der Waals density functional theory calculations of water on graphene for both individual water molecules and continuous water layers with coverage ranging from one to eight monolayers. Furthermore, we have paid attention to the influence of the water molecule orientation toward graphene on its doping properties. In this article, we present the results of the band structure and the Bader charge analysis, showing the p-doping of graphene can be synergistically enhanced by putting 4-8 layers of an ice-like water structure on graphene having the water molecules oriented with oxygen atoms toward graphene.

Density functional study of gallium clusters on graphene: electronic doping and diffusion.

Motivated by experimental results on transport properties of graphene covered by gallium atoms, the density functional theory study of clustering of gallium atoms on graphene (up to a size of 8 atoms) is presented. The paper explains a rapid initial increase of graphene electron doping by individual Ga atoms with Ga coverage, which is continually reduced to zero, when bigger multiple-atom clusters have been formed. According to density functional theory calculations with and without the van der Waals correction, gallium atoms start to form a three-dimensional cluster from five and three atoms, respectively. The results also explain an easy diffusion of Ga atoms while forming clusters caused by a small diffusion barrier of 0.11 eV. Moreover, the calculations show this barrier can be additionally reduced by the application of an external electric field, which was simulated by the ionization of graphene. This effect offers a unique possibility to control the cluster size in experiments only by applying a gate-voltage to the graphene in a field-effect transistor geometry and thereby without growth temperature assistance.

Long Non-Coding RNAs - Current Methods of Detection and Clinical Applications.

BACKGROUND: Long non-coding RNAs (lncRNA) are more than 200-nucleotide-long RNA molecules that affect multiple physiologic phenomena and have important regulatory functions in cells. Their levels are often altered in various malignancies, thus they represent a potential biomarker for the diagnostics, prognosis or recurrence of cancer. Their importance has recently led to an enormous increase in a number of publications on the subject. The most frequently studied lncRNAs are HOTAIR, MALAT1 and PCA3. AIM: Numerous methods are currently being developed for the analysis or detection of lncRNA. They are mostly based on optical methods used for the detection of messenger RNAs, including polymerase chain reaction with reverse transcription, fluorescence in situ hybridisation or next-generation sequencing, but caution must be taken due to their structural differences. Here, we describe not only standard but also novel techniques for lncRNA detection, including chemiluminescent and electrochemical techniques. CONCLUSION: Despite the great progress and plethora of papers on this topic, there is only one single approved lncRNA-based diagnostic test, a PCA3 test for the diagnosis of prostate cancer from the patients urine. All other tests are only in their research phase and need to be validated. Nevertheless, lncRNA diagnostics offer enormous potential and thus it is highly probable that other diagnostic tests on different lncRNA types will soon appear.

Fracture toughness and structural evolution in the TiAlN system upon annealing.

Hard coatings used to protect engineering components from external loads and harsh environments should ideally be strong and tough. Here we study the fracture toughness, K IC, of Ti1-xAlxN upon annealing by employing micro-fracture experiments on freestanding films. We found that K IC increases by about 11% when annealing the samples at 900 °C, because the decomposition of the supersaturated matrix leads to the formation of nanometer-sized domains, precipitation of hexagonal-structured B4 AlN (with their significantly larger specific volume), formation of stacking faults, and nano-twins. In contrast, for TiN, where no decomposition processes and formation of nanometer-sized domains can be initiated by an annealing treatment, the fracture toughness K IC remains roughly constant when annealed above the film deposition temperature. As the increase in K IC found for Ti1-xAlxN upon annealing is within statistical errors, we carried out complementary cube corner nanoindentation experiments, which clearly show reduced (or even impeded) crack formation for annealed Ti1-xAlxN as compared with their as-deposited counterpart. The ability of Ti1-xAlxN to maintain and even increase the fracture toughness up to high temperatures in combination with the concomitant age hardening effects and excellent oxidation resistance contributes to the success of this type of coatings.

Electronic transport properties of graphene doped by gallium.

In this work we present the effect of low dose gallium (Ga) deposition (<4 ML) performed in UHV (10-7 Pa) on the electronic doping and charge carrier scattering in graphene grown by chemical vapor deposition. In situ graphene transport measurements performed with a graphene field-effect transistor structure show that at low Ga coverages a graphene layer tends to be strongly n-doped with an efficiency of 0.64 electrons per one Ga atom, while the further deposition and Ga cluster formation results in removing electrons from graphene (less n-doping). The experimental results are supported by the density functional theory calculations and explained as a consequence of distinct interaction between graphene and Ga atoms in case of individual atoms, layers, or clusters.

[Analysis of DNA Methylation in BRCA2 Gene Using Electrode Biochips]. / Stanovení DNA metylace v BRCA2 genu na elektrodových biocipech.

BACKGROUND: Since DNA methylation results in gene silencing, it plays an important role in cell proliferation and differentiation. Abnormal DNA methylation is often associated with carcinogenesis, and therefore its analysis could be an interesting option in early diagnostics of cancer, determination of tumour invasiveness, progression or metastatic potential. One of the methods for DNA analysis could be also electrochemistry, which offers inexpensive instrumentation, short measurement times and parallel detection of samples. MATERIAL AND METHODS: We have analyzed methylation status of a DNA site within BRCA2 gene promoter sequence, which is associated with breast cancer. We hybridized this sequence at magnetic beads and then we incubated them with methylation-sensitive restriction endonuclease BstUI, which specifically cleaves non-methylated restriction site CGCG, but not methylated one. After addition of labeled DNA probe and peroxidase, we monitored enzymatic reaction at the electrode chip. RESULTS: First, we tested suitability of designed DNA probes and effectiveness of BstUI cleavage using gel electrophoresis. Afterwards, we applied these probes and the enzyme to the magnetic beads, with the final detection at the electrode chip. We show good correlation of electrochemical and electrophoresis results, i.e. that labelled DNA probe was removed only when DNA containing non-methylated restriction site was incubated with BstUI. When this restriction site was methylated, no cleavage occurred and the resulting signal was high. We also show good reproducibility of the measurement. CONCLUSION: Electrochemical detection, in combination with magnetic beads and restriction enzymes, could be a potentially useful tool for determination of methylation status of a specific DNA sequence.Key words: DNA methylation - DNA restriction enzymes - electrochemistry - nucleic acid hybridization This work was supported by MEYS - NPS I - LO1413. The authors declare they have no potential conflicts of interest concerning drugs, products, or services used in the study. The Editorial Board declares that the manuscript met the ICMJE recommendation for biomedical papers.Submitted: 6. 3. 2017Accepted: 26. 3. 2017.

[Novel Approaches in DNA Methylation Studies - MS-HRM Analysis and Electrochemistry]. / Nové metody studia metylace DNA - MS-HRM analýza a elektrochemie.

Cytosine methylation in DNA is an epigenetic mechanism regulating gene expression and plays a vital role in cell differentiation or proliferation. Tumor cells often exhibit aberrant DNA methylation, e.g. hypermethylation of tumor suppressor gene promoters. New methods, capable of determining methylation status of specific DNA sequences, are thus being developed. Among them, MS-HRM (methylation-specific high resolution melting) and electrochemistry offer relatively inexpensive instrumentation, fast assay times and possibility of screening multiple samples/DNA regions simultaneously. MS-HRM is due to its sensitivity and simplicity an interesting alternative to already established techniques, including methylation-specific PCR or bisulfite sequencing. Electrochemistry, when combined with suitable electroactive labels and electrode surfaces, has been applied in several unique strategies for discrimination of cytosines and methylcytosines. Both techniques were successfully tested in analysis of DNA methylation within promoters of important tumor suppressor genes and could thus help in achieving more precise diagnostics and prognostics of cancer. Aberrant methylation of promoters has already been described in hundreds of genes associated with tumorigenesis and could serve as important biomarker if new methods applicable into clinical practice are sufficiently advanced.Key words: DNA methylation - 5-methylcytosine - HRM analysis - melting temperature - DNA duplex - electrochemistry - nucleic acid hybridizationThis work was supported by MEYS - NPS I - LO1413.The authors declare they have no potential conflicts of interest concerning drugs, products, or services used in the study.The Editorial Board declares that the manuscript met the ICMJE recommendation for biomedical papers.Submitted: 6. 5. 2016Accepted: 16. 5. 2016.

Electrochemical analysis of a novel ferrocene derivative as a potential antitumor drug.

Ferrocenes represent an interesting group of drugs with potential antitumor properties. Moreover, their electronic properties make them suitable for electrochemical studies. We determined an uptake of a novel ferrocene derivative in low µM concentrations by selected cancer cell lines and showed its localization predominantly in cytoplasm, using glassy carbon electrodes.

Complementary ab initio and X-ray nanodiffraction studies of Ta2O5.

The complex structure of Ta2O5 led to the development of various structural models. Among them, superstructures represent the most stable configurations. However, their formation requires kinetic activity and long-range ordering processes, which are hardly present during physical vapor deposition. Based on nano-beam X-ray diffraction and concomitant ab initio studies, a new metastable orthorhombic basic structure is introduced for Ta2O5 with lattice parameters a = 6.425 Å, b = 3.769 Å and c = 7.706 Å. The unit cell containing only 14 atoms, i.e. two formula unit blocks in the c direction, is characterized by periodically alternating the occupied oxygen site between two possible positions in succeeding 002-planes. This structure can be described by the space group 53 (Pncm) with four Wyckoff positions, and exhibits an energy of formation of -3.209 eV atom-1. Among all the reported basic structures, its energy of formation is closest to those of superstructures. Furthermore, this model exhibits a 2.5 eV band gap, which is closer to experimental data than the band gap of any other basic-structure model. The sputtered Ta2O5 films develop only a superstructure if annealed at temperatures >800 °C in air or vacuum. Based on these results and the conveniently small unit cell size, it is proposed that the basic-structure model described here is an ideal candidate for both structure and electronic state descriptions of orthorhombic Ta2O5 materials.

Dietary exposure to aflatoxins, ochratoxin A and deoxynivalenol from a total diet study in an adult urban Lebanese population.

Exposure to mycotoxins may be associated with carcinogenic, immunosuppressant and estrogenic effects. In the Middle-East, studies investigating food contamination and dietary exposure to mycotoxins are particularly scarce. This study aims at evaluating the dietary exposure of an adult Lebanese urban population to four mycotoxins (AFB1, AFM1, OTA, DON) classified as priority food contaminants by the WHO. Dietary exposure assessment was performed by means of the total diet study approach. Average and excessive consumer exposure estimates (p95) were calculated and compared with appropriate toxicological reference values (TRVs). Average dietary exposure levels to OTA and DON represented 29.9% and 156.8% of the respective TRVs, with the p95 exposure estimates approaching or exceeding the TRVs for these mycotoxins (95.1% and 355.8%, respectively). Based on the mean dietary exposure level to AFB1, cancer risk was estimated at 0.0527-0.0545cases/100,000persons/year, while mean exposure to AFM1 was associated with a population risk of 0.0018-0.0027cases/100,000persons/year. The study's findings place Lebanon among countries that are highly exposed to mycotoxins through the diet and call for larger-scale studies aiming at providing a comprehensive assessment of the dietary exposure of the Lebanese population to mycotoxins as well as to other food contaminants.

[Electrochemical analysis of nucleic acids, proteins and polysaccharides in biomedicine]. / Elektrochemická analýza nukleových kyselin, bílkovin a polysacharidu v bio-medicíne

Electrochemical analysis of nucleic acids, proteins and polysaccharides represents an interesting, although not widely spread alternative to current methods based predominantly on optical detection because it offers a relatively inexpensive, fast and instrumentally simple detection of parallel samples on miniaturized chips, ideal for personalized medicine of the 21st century. Nucleic acid electrochemistry enables, for example, detection of specific DNA sequences (for determination of genes or presence of bacteria and viruses, etc.), DNA damage analysis and interaction with other molecules, DNA methylation or detection of microRNAs as potential cancer bio-markers. In the electrochemistry of proteins, great emphasis is put on construction of immunosensors for capturing specific proteins (antigens) using antibodies, suitable for diagnostics. From a bio-physical point of view, intrinsic electrocatalytic signal of proteins sensitive to conformational changes could be useful in discrimination of mutant proteins (e. g. p53), native and aggregated forms (α-synuclein in Parkinsons disease) or for studies of protein interactions with low molecular  weight ligands and DNA. Due to an increased interest of scientists in glycoproteins, new electrochemical papers emerged aiming at detection of oligosaccharides and polysaccharides (i.e. glycans, when part of the protein). These assays employ for instance electroactive labels specific for saccharides or lectin bio-sensors using lectins which strongly bind glycans. Electrochemical analysis thus appears as an interesting tool in current genomics, proteomics and glycomics, as well as for cancer diagnostics.

Structural and mechanical evolution of reactively and non-reactively sputtered Zr-Al-N thin films during annealing.

The influence of reactive and non-reactive sputtering on structure, mechanical properties, and thermal stability of Zr1 - xAlxN thin films during annealing to 1500 °C is investigated in detail. Reactive sputtering of a Zr0.6Al0.4 target leads to the formation of Zr0.66Al0.34N thin films, mainly composed of supersaturated cubic (c) Zr1 - xAlxN with small fractions of (semi-)coherent wurtzite (w) AlN domains. Upon annealing, the formation of cubic Zr-rich domains and growth of the (semi-)coherent w-AlN domains indicate spinodal-like decomposition. Loss of coherency can only be observed for annealing temperatures above 1150 °C. Following these decomposition processes, the hardness remains at the as-deposited value of ~ 29 GPa with annealing up to 1100 °C. Using a ceramic (ZrN)0.6(AlN)0.4 target and sputtering in Ar atmosphere allows preparing c-Zr0.68Al0.32N coatings with a well-defined crystalline single-phase cubic structure combined with higher hardnesses of ~ 31 GPa. Due to the absence of (semi-)coherent w-AlN domains in the as-deposited state, which could act as nucleation sites, the decomposition process of c-Zr1 - xAlxN is retarded. Only after annealing at 1270 °C, the formation of incoherent w-AlN can be detected. Hence, their hardness remains very high with ~ 33 GPa even after annealing at 1200 °C. The study highlights the importance of controlling the deposition process to prepare well-defined coatings with high mechanical properties and thermal stability.

Lateral gradients of phases, residual stress and hardness in a laser heated Ti0.52Al0.48N coating on hard metal.

The influence of a local thermal treatment on the properties of Ti-Al-N coatings is not understood. In the present work, a Ti0.52Al0.48N coating on a WC-Co substrate was heated with a diode laser up to 900 °C for 30 s and radially symmetric lateral gradients of phases, residual stress and hardness were characterized ex-situ using position-resolved synchrotron X-ray diffraction, Raman spectroscopy, transmission electron microscopy and nanoindentation. The results reveal (i) a residual stress relaxation at the edge of the irradiated area and (ii) a compressive stress increase of few GPa in the irradiated area center due to the Ti-Al-N decomposition, in particular due to the formation of small wurtzite (w) AlN domains. The coating hardness increased from 35 to 47 GPa towards the center of the heated spot. In the underlying heated substrate, a residual stress change from about - 200 to 500 MPa down to a depth of 6 µm is observed. Complementary, in-situ high-temperature X-ray diffraction analysis of stresses in a homogeneously heated Ti0.52Al0.48N coating on a WC-Co substrate was performed in the range of 25-1003 °C. The in-situ experiment revealed the origin of the observed thermally-activated residual stress oscillation across the laser heated spot. Finally, it is demonstrated that the coupling of laser heating to produce lateral thermal gradients and position-resolved experimental techniques opens the possibility to perform fast screening of structure-property relationships in complex materials.