Modeling Water Interactions with Graphene and Graphite via Force Fields Consistent with Experimental Contact Angles.

Accurate simulation models for water interactions with graphene and graphite are important for nanofluidic applications, but existing force fields produce widely varying contact angles. Our extensive review of the experimental literature reveals extreme variation among reported values of graphene-water contact angles and a clustering of graphite-water contact angles into groups of freshly exfoliated (60° ± 13°) and not-freshly exfoliated graphite surfaces. The carbon-oxygen dispersion energy for a classical force field is optimized with respect to this 60° graphite-water contact angle in the infinite-force-cutoff limit, which in turn yields a contact angle for unsupported graphene of 80°, in agreement with the mean of the experimental results. Interaction force fields for finite cutoffs are also derived. A method for calculating contact angles from pressure tensors of planar equilibrium simulations that is ideally suited to graphite and graphene surfaces is introduced. Our methodology is widely applicable to any liquid-surface combination.

Collective modes and quantum effects in two-dimensional nanofluidic channels.

Nanoscale fluid transport is typically pictured in terms of atomic-scale dynamics, as is natural in the real-space framework of molecular simulations. An alternative Fourier-space picture, that involves the collective charge fluctuation modes of both the liquid and the confining wall, has recently been successful at predicting new nanofluidic phenomena such as quantum friction and near-field heat transfer, that rely on the coupling of those fluctuations. Here, we study the charge fluctuation modes of a two-dimensional (planar) nanofluidic channel. Introducing confined response functions that generalize the notion of surface response function, we show that the channel walls exhibit coupled plasmon modes as soon as the confinement is comparable to the plasmon wavelength. Conversely, the water fluctuations remain remarkably bulk-like, with significant confinement effects arising only when the wall spacing is reduced to 7 Å. We apply the confined response formalism to predict the dependence of the solid-water quantum friction and thermal boundary conductance on channel width for model channel wall materials. Our results provide a general framework for Coulomb interactions of fluctuating matter under nanoscale confinement.

Multiscale Modeling of Aqueous Electric Double Layers.

From the stability of colloidal suspensions to the charging of electrodes, electric double layers play a pivotal role in aqueous systems. The interactions between interfaces, water molecules, ions and other solutes making up the electrical double layer span length scales from Ångströms to micrometers and are notoriously complex. Therefore, explaining experimental observations in terms of the double layer's molecular structure has been a long-standing challenge in physical chemistry, yet recent advances in simulations techniques and computational power have led to tremendous progress. In particular, the past decades have seen the development of a multiscale theoretical framework based on the combination of quantum density functional theory, force-field based simulations and continuum theory. In this Review, we discuss these theoretical developments and make quantitative comparisons to experimental results from, among other techniques, sum-frequency generation, atomic-force microscopy, and electrokinetics. Starting from the vapor/water interface, we treat a range of qualitatively different types of surfaces, varying from soft to solid, from hydrophilic to hydrophobic, and from charged to uncharged.

Enhanced interfacial water dissociation on a hydrated iron porphyrin single-atom catalyst in graphene.

Single Atom Catalysis (SAC) is an expanding field of heterogeneous catalysis in which single metallic atoms embedded in different materials catalyze a chemical reaction, but these new catalytic materials still lack fundamental understanding when used in electrochemical environments. Recent characterizations of non-noble metals like Fe deposited on N-doped graphitic materials have evidenced two types of Fe-N4 fourfold coordination, either of pyridine type or of porphyrin type. Here, we study these defects embedded in a graphene sheet and immersed in an explicit aqueous medium at the quantum level. While the Fe-pyridine SAC model is clear cut and widely studied, it is not the case for the Fe-porphyrin SAC that remains ill-defined, because of the necessary embedding of odd-membered rings in graphene. We first propose an atomistic model for the Fe-porphyrin SAC. Using spin-polarized ab initio molecular dynamics, we show that both Fe SACs spontaneously adsorb two interfacial water molecules from the solvent on opposite sides. Interestingly, we unveil a different catalytic reactivity of the two hydrated SAC motives: while the Fe-porphyrin defect eventually dissociates an adsorbed water molecule under a moderate external electric field, the Fe-pyridine defect does not convey water dissociation.

MicroRNAs in Tumor Endothelial Cells: Regulation, Function and Therapeutic Applications.

Tumor endothelial cells (TECs) are key stromal components of the tumor microenvironment, and are essential for tumor angiogenesis, growth and metastasis. Accumulating evidence has shown that small single-stranded non-coding microRNAs (miRNAs) act as powerful endogenous regulators of TEC function and blood vessel formation. This systematic review provides an up-to-date overview of these endothelial miRNAs. Their expression is mainly regulated by hypoxia, pro-angiogenic factors, gap junctions and extracellular vesicles, as well as long non-coding RNAs and circular RNAs. In preclinical studies, they have been shown to modulate diverse fundamental angiogenesis-related signaling pathways and proteins, including the vascular endothelial growth factor (VEGF)/VEGF receptor (VEGFR) pathway; the rat sarcoma virus (Ras)/rapidly accelerated fibrosarcoma (Raf)/mitogen-activated protein kinase kinase (MEK)/extracellular signal-regulated kinase (ERK) pathway; the phosphoinositide 3-kinase (PI3K)/AKT pathway; and the transforming growth factor (TGF)-ß/TGF-ß receptor (TGFBR) pathway, as well as krüppel-like factors (KLFs), suppressor of cytokine signaling (SOCS) and metalloproteinases (MMPs). Accordingly, endothelial miRNAs represent promising targets for future anti-angiogenic cancer therapy. To achieve this, it will be necessary to further unravel the regulatory and functional networks of endothelial miRNAs and to develop safe and efficient TEC-specific miRNA delivery technologies.

SIRT1 regulates DNA damage signaling through the PP4 phosphatase complex.

The Sirtuin family of NAD+-dependent enzymes plays an important role in maintaining genome stability upon stress. Several mammalian Sirtuins have been linked directly or indirectly to the regulation of DNA damage during replication through Homologous recombination (HR). The role of one of them, SIRT1, is intriguing as it seems to have a general regulatory role in the DNA damage response (DDR) that has not yet been addressed. SIRT1-deficient cells show impaired DDR reflected in a decrease in repair capacity, increased genome instability and decreased levels of γH2AX. Here we unveil a close functional antagonism between SIRT1 and the PP4 phosphatase multiprotein complex in the regulation of the DDR. Upon DNA damage, SIRT1 interacts specifically with the catalytical subunit PP4c and promotes its inhibition by deacetylating the WH1 domain of the regulatory subunits PP4R3α/ß. This in turn regulates γH2AX and RPA2 phosphorylation, two key events in the signaling of DNA damage and repair by HR. We propose a mechanism whereby during stress, SIRT1 signaling ensures a global control of DNA damage signaling through PP4.

Effects of above ground pathogen infection and fungicide application on the root-associated microbiota of apple saplings.

BACKGROUND: The root-associated microbiome has been of keen research interest especially in the last decade due to the large potential for increasing overall plant performance in agricultural systems. Knowledge about the impact of above ground plant disturbances on the root-associated microbiome remains limited. We addressed this by focusing on two potential impacts, foliar pathogen infection alone and in combination with the application of a plant health protecting product. We hypothesized that these lead to plant-mediated responses in the rhizosphere microbiota. RESULTS: The effects of an infection of greenhouse grown apple saplings with either Venturia inaequalis or Podosphaera leucotricha as foliar pathogen, as well as the combined effect of P. leucotricha infection and foliar application of the synthetic plant health protecting product Aliette (active ingredient: fosetyl-aluminum), were studied on the root-associated microbiota. The bacterial community structure of rhizospheric soil and endospheric root material was characterized post-infection, using 16S rRNA gene amplicon sequencing. With increasing disease severity both pathogens led to changes in the rhizosphere and endosphere bacterial communities in comparison to uninfected plants (explained variance up to 17.7%). While the preventive application of Aliette on healthy plants two weeks prior inoculation did not induce changes in the root-associated microbiota, a second later application on the diseased plants decreased disease severity and resulted in differences of the rhizosphere bacterial community between infected and several of the cured plants, though differences were overall not statistically significant. CONCLUSIONS: Foliar pathogen infections can induce plant-mediated changes in the root-associated microbiota, indicating that above ground disturbances are reflected in the below-ground microbiome, even though these become evident only upon severe leaf infection. The application of the fungicide Aliette on healthy plants itself did not induce any changes, but the application to diseased plants helped the plant to regain the microbiota of a healthy plant. These findings indicate that above ground agronomic management practices have implications for the root-associated microbiome, which should be considered in the context of microbiome management strategies.

Electrokinetic, electrochemical, and electrostatic surface potentials of the pristine water liquid-vapor interface.

Although conceptually simple, the air-water interface displays rich behavior and is subject to intense experimental and theoretical investigations. Different definitions of the electrostatic surface potential as well as different calculation methods, each relevant for distinct experimental scenarios, lead to widely varying potential magnitudes and sometimes even different signs. Based on quantum-chemical density-functional-theory molecular dynamics (DFT-MD) simulations, different surface potentials are evaluated and compared to force-field (FF) MD simulations. As well explained in the literature, the laterally averaged electrostatic surface potential, accessible to electron holography, is dominated by the trace of the water molecular quadrupole moment, and using DFT-MD amounts to +4.35 V inside the water phase, very different from results obtained with FF water models which yield negative values of the order of -0.4 to -0.6 V. Thus, when predicting potentials within water molecules, as relevant for photoelectron spectroscopy and non-linear interface-specific spectroscopy, DFT simulations should be used. The electrochemical surface potential, relevant for ion transfer reactions and ion surface adsorption, is much smaller, less than 200 mV in magnitude, and depends specifically on the ion radius. Charge transfer between interfacial water molecules leads to a sizable surface potential as well. However, when probing electrokinetics by explicitly applying a lateral electric field in DFT-MD simulations, the electrokinetic ζ-potential turns out to be negligible, in agreement with predictions using continuous hydrodynamic models. Thus, interfacial polarization charges from intermolecular charge transfer do not lead to significant electrokinetic mobility at the pristine vapor-liquid water interface, even assuming these transfer charges are mobile in an external electric field.

Spatio-temporal variation in the root-associated microbiota of orchard-grown apple trees.

BACKGROUND: The root-associated microbiome has been of keen research interest especially in the last decade due to the large potential for increasing overall plant performance in agricultural systems. Studies about spatio-temporal variation of the root-associated microbiome focused so far primarily on community-compositional changes of annual plants, while little is known about their perennial counterparts. The aim of this work was to get deep insight into the spatial patterns and temporal dynamics of the root associated microbiota of apple trees. RESULTS: The bacterial community structure in rhizospheric soil and endospheric root material from orchard-grown apple trees was characterized based on 16S rRNA gene amplicon sequencing. At the small scale, the rhizosphere and endosphere bacterial communities shifted gradually with increasing root size diameter (PERMANOVA R2-values up to 0.359). At the larger scale, bulk soil heterogeneity introduced variation between tree individuals, especially in the rhizosphere microbiota, while the presence of a root pathogen was contributing to tree-to-tree variation in the endosphere microbiota. Moreover, the communities of both compartments underwent seasonal changes and displayed year-to-year variation (PERMANOVA R2-values of 0.454 and 0.371, respectively). CONCLUSIONS: The apple tree root-associated microbiota can be spatially heterogeneous at field scale due to soil heterogeneities, which particularly influence the microbiota in the rhizosphere soil, resulting in tree-to-tree variation. The presence of pathogens can contribute to this variation, though primarily in the endosphere microbiota. Smaller-scale spatial heterogeneity is observed in the rhizosphere and endosphere microbiota related to root diameter, likely influenced by root traits and processes such as rhizodeposition. The microbiota is also subject to temporal variation, including seasonal effects and annual variation. As a consequence, responses of the tree root microbiota to further environmental cues should be considered in the context of this spatio-temporal variation.

Hydrophobicity of Self-Assembled Monolayers of Alkanes: Fluorination, Density, Roughness, and Lennard-Jones Cutoffs.

The interplay of fluorination and structure of alkane self-assembled monolayers and how these affect hydrophobicity are explored via molecular dynamics simulations, contact angle goniometry, and surface-enhanced infrared absorption spectroscopy. Wetting coefficients are found to grow linearly in the monolayer density for both alkane and perfluoroalkane monolayers. The larger contact angles of monolayers of perfluorinated alkanes are shown to be primarily caused by their larger molecular volume, which leads to a larger nearest-neighbor grafting distance and smaller tilt angle. Increasing the Lennard-Jones force cutoff in simulations is found to increase hydrophilicity. Specifically, wetting coefficients scale like the inverse square of the cutoff, and when extrapolated to the infinite cutoff limit, they yield contact angles that compare favorably to experimental values. Nanoscale roughness is also found to reliably increase monolayer hydrophobicity, mostly via the reduction of the entropic part of the work of adhesion. Analysis of depletion lengths shows that droplets on nanorough surfaces partially penetrate the surface, intermediate between Wenzel and Cassie-Baxter states.

The Hydrotropic Effect of Ionic Liquids in Water-in-Salt Electrolytes*.

Water-in-salt electrolytes have successfully expanded the electrochemical stability window of aqueous electrolytes beyond 2 V. Further improvements in stability can be achieved by partially substituting water with either classical organic solvents or ionic liquids. Here, we study ternary electrolytes composed of LiTFSI, water, and imidazolium ionic liquids. We find that the LiTFSI solubility strongly increases from 21 mol kg-1 in water to up to 60 mol kg-1 in the presence of ionic liquid. The solution structure is investigated with Raman and NMR spectroscopy and the enhanced LiTFSI solubility is found to originate from a hydrotropic effect of the ionic liquids. The increased reductive stability of the ternary electrolytes enables stable cycling of an aqueous lithium-ion battery with an energy density of 150 Wh kg-1 on the active material level based on commercially relevant Li4 Ti5 O12 and LiNi0.8 Mn0.1 Co0.1 O2 electrode materials.

Fractal Geometry of Higher Derivative Gravity.

We determine the scaling properties of geometric operators such as lengths, areas, and volumes in models of higher derivative quantum gravity by renormalizing appropriate composite operators. We use these results to deduce the fractal dimensions of such hypersurfaces embedded in a quantum spacetime at very small distances.

The Impact of Halogenated Phenylalanine Derivatives on NFGAIL Amyloid Formation.

The hexapeptide hIAPP22-27 (NFGAIL) is known as a crucial amyloid core sequence of the human islet amyloid polypeptide (hIAPP) whose aggregates can be used to better understand the wild-type hIAPP's toxicity to ß-cell death. In amyloid research, the role of hydrophobic and aromatic-aromatic interactions as potential driving forces during the aggregation process is controversially discussed not only in case of NFGAIL, but also for amyloidogenic peptides in general. We have used halogenation of the aromatic residue as a strategy to modulate hydrophobic and aromatic-aromatic interactions and prepared a library of NFGAIL variants containing fluorinated and iodinated phenylalanine analogues. We used thioflavin T staining, transmission electron microscopy (TEM) and small-angle X-ray scattering (SAXS) to study the impact of side-chain halogenation on NFGAIL amyloid formation kinetics. Our data revealed a synergy between aggregation behavior and hydrophobicity of the phenylalanine residue. This study introduces systematic fluorination as a toolbox to further investigate the nature of the amyloid self-assembly process.

Water-in-salt electrolytes for aqueous lithium-ion batteries with liquidus temperatures below -10 °C.

Crystallization near room temperature is a common challenge for water-in-salt electrolytes. We demonstrate that water-in-salt electrolytes based on lithium (pentafluoroethanesulfonyl)(trifluoromethanesulfonyl)imide remain thermodynamically in the liquid state down to at least -10 °C. Combined with their excellent chemical and electrochemical stability as well as high lithium-ion conductivity, these electrolytes represent a key enabler for the next generation of high-voltage aqueous lithium-ion batteries.

Unraveling the Formation Mechanism of Solid-Liquid Electrolyte Interphases on LiPON Thin Films.

Most commercial lithium-ion batteries and other types of batteries rely on liquid electrolytes, which are preferred because of their high ionic conductivity, and facilitate fast charge-transfer kinetics at the electrodes. On the other hand, hybrid battery concepts that combine solid and liquid electrolytes might be needed to suppress unwanted shuttle effects in liquid electrolyte-only systems, in particular if mobile redox systems are involved in the cell chemistry. However, at the then newly introduced interface between liquid and solid electrolytes, a solid-liquid electrolyte interphase forms. In this study, we analyze the formation of such an interphase between the solid electrolyte lithium phosphorous oxide nitride (Li xPO yN z, "LiPON") and various liquid electrolytes using in situ neutron reflectometry, quartz crystal microbalance, and atomic force microscopy measurements. Our results show that the interphase consists of two layers: a nonconducting layer directly in contact with "LiPON" and a lithium-rich outer layer. Initially, a fast growth of the solid-liquid electrolyte interphase is observed, which slows down significantly afterward, resulting in a thickness of about 20 nm eventually. Here, a formation mechanism is proposed, which describes the solid-liquid electrolyte interphase growth as the fast deposition of a film, which mostly covers the "LiPON", with only a little degree of remaining porosity. The residual void space is then slowly filled, thus blocking the remaining channels for ionic conduction, which leads to increasing resistance of the interphase. The results obtained imply that hybrid battery concepts with liquid electrolyte and solid electrolyte can be hampered by highly resistive interphases, whose formation cannot be simply slowed down or suppressed. Further research is required regarding possible countermeasures.

A rapid identification technique for drug-resistant Mycobacterium tuberculosis isolates using mismatch specific cleavage enzyme.

The emergence of multidrug-resistant tuberculosis (MDR-TB) and extensively drug-resistant tuberculosis (XDR-TB) strains is a major health problem for high Tuberculosis (TB) incidence countries. Therefore, it is of interest to identify antibiotic resistant bacteria by mismatch detection using DNA hybridization. We generated PCR products for five genes (rpoB, inhA, katG, gyrA and rrs) associated with drug resistance TB from MDR and XDR Mycobacterium tuberculosis (MTB) DNA samples. These were hybridized to PCR products from MTB H37Rv (pansusceptible laboratory strain) to generate DNA hetero-duplex products, which was digested by Detection Enzyme (GeneArt Genomic Cleavage Detection Kit) and visualized by agarose gel electrophoresis. Results show different bands with sizes of 400 bp and 288 bp (rpoB), 280 bp (inhA), 310 bp (katG), 461 bp (gyrA) and 427 bp (rrs) suggesting mutations in DNA heteroduplex for each gene. Detection Enzyme specifically cleaves DNA hetero-duplex with mismatch. The technique helps in the improved detection of MDR (mutations in rpoB, inhA and katG) and XDR (mutations in rpoB, inhA katG, gyrA and rrs) MTB strains. Moreover, the technique is customized without expensive specialized equipment to detect mutations. It is also fast, efficient and easy to implement in standard molecular biology laboratories.

Local control of globally competing patterns in coupled Swift-Hohenberg equations.

We present analytical and numerical investigations of two anti-symmetrically coupled 1D Swift-Hohenberg equations (SHEs) with cubic nonlinearities. The SHE provides a generic formulation for pattern formation at a characteristic length scale. A linear stability analysis of the homogeneous state reveals a wave instability in addition to the usual Turing instability of uncoupled SHEs. We performed weakly nonlinear analysis in the vicinity of the codimension-two point of the Turing-wave instability, resulting in a set of coupled amplitude equations for the Turing pattern as well as left- and right-traveling waves. In particular, these complex Ginzburg-Landau-type equations predict two major things: there exists a parameter regime where multiple different patterns are stable with respect to each other and that the amplitudes of different patterns interact by local mutual suppression. In consequence, different patterns can coexist in distinct spatial regions, separated by localized interfaces. We identified specific mechanisms for controlling the position of these interfaces, which distinguish what kinds of patterns the interface connects and thus allow for global pattern selection. Extensive simulations of the original SHEs confirm our results.

A Molecular and Cytogenetic Update on Non-Small Cell Lung Carcinoma.

Lung cancer is one of the leading causes of cancer-related death worldwide. Among patients with lung cancer, approximately 85% have non-small cell lung carcinoma (NSCLC). The discovery of oncogenic driver mutations in NSCLC opened new personalized treatment options. Several methods that can identify these biomarkers are used routinely in a clinical setting to stratify patients for targeted therapy. In this review, we summarize the most clinically relevant driver genes, discuss the advantages and limitations of current clinical detection methods, and highlight the benefits of personalized treatment over standard chemotherapy.

The t(12;21)(p13;q22) in Pediatric B-Acute Lymphoblastic Leukemia: An Update.

Erratum: Figure 1 on the last edition The Journal of the Association of Genetic Technologists. 2017;43(3): 113-127 does not contain the derivative 21. We are replacing this figure with the present one. In the section Secondary genetic aberrations we would like to add that: Deletions of 11q23 are observed in 5-6% of cases (Raynaud et al., 1999; Attarbaschi et al., 2004; Alvarez et al., 2005; Forestier et al., 2007).

The t(12;21)(p13;q22) in Pediatric B-Acute Lymphoblastic Leukemia: An Update.

Pediatric B-cell acute lymphoblastic leukemia (B-ALL) is the most common hematological malignancy in children, and the t(12;21)(p13;q22) occurs in approximately 25% of these cases, making it is the most prevalent chromosomal abnormality. The t(12;21) which disrupts hematopoietic differentiation and proliferation, and can be present as a sole abnormality or within the context of a complex karyotype characterized by three or more chromosomal abnormalities. The prognosis of t(12;21) within a complex karyotype is extensively debated. In this review, we discuss the literature regarding t(12;21) and summarize the cytogenetic features found in 363 pediatric cases compiled from the Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer. Cytogenetically, most of the cases had secondary chromosomal abnormalities, about half of which were in the context of a complex karyotype. Trisomy 21 was found to be the most common numerical abnormality in almost one-fifth of the cases, and deletions on chromosome 12 and 6 occurred in 16.9% and 12.5% of cases, respectively. In general, t(12;21) in B-ALL is associated with a favorable prognosis. Herein, we found no significant difference in survival outcome of t(12;21) with a on-complex or complex karyotype.