Visual verification and analysis of cluster detection for molecular dynamics

A current research topic in molecular thermodynamics is the condensation of vapor to liquid and the investigation of this process at the molecular level. Condensation is found in many physical phenomena, e.g. the formation of atmospheric clouds or the processes inside steam turbines, where a detailed knowledge of the dynamics of condensation processes will help to optimize energy efficiency and avoid problems with droplets of macroscopic size. The key properties of these processes are the nucleation rate and the critical cluster size. For the calculation of these properties it is essential to make use of a meaningful definition of molecular clusters, which currently is a not completely resolved issue. In this paper a framework capable of interactively visualizing molecular datasets of such nucleation simulations is presented, with an emphasis on the detected molecular clusters. To check the quality of the results of the cluster detection, our framework introduces the concept of flow groups to highlight potential cluster evolution over time which is not detected by the employed algorithm. To confirm the findings of the visual analysis, we coupled the rendering view with a schematic view of the clusters' evolution. This allows to rapidly assess the quality of the molecular cluster detection algorithm and to identify locations in the simulation data in space as well as in time where the cluster detection fails. Thus, thermodynamics researchers can eliminate weaknesses in their cluster detection algorithms. Several examples for the effective and efficient usage of our tool are presented.     

Toward High‐Dimensional Single‐Cell Analysis of Graphene Oxide Biological Impact: Tracking on Immune Cells by Single‐Cell Mass Cytometry

Considering the potential exposure to graphene, the most investigated nanomaterial, the assessment of the impact on human health has become an urgent need. The deep understanding of nanomaterial safety is today possible by high‐throughput single‐cell technologies. Single‐cell mass cytometry (cytometry by time‐of flight, CyTOF) shows an unparalleled ability to phenotypically and functionally profile complex cellular systems, in particular related to the immune system, as recently also proved for graphene impact. The next challenge is to track the graphene distribution at the single‐cell level. Therefore, graphene oxide (GO) is functionalized with AgInS₂ nanocrystals (GO–In), allowing to trace GO immune–cell interactions via the indium (¹¹⁵In) channel. Indium is specifically chosen to avoid overlaps with the commercial panels (>30 immune markers). As a proof of concept, the GO–In CyTOF tracking is performed at the single‐cell level on blood immune subpopulations, showing the GO interaction with monocytes and B cells, therefore guiding future immune studies. The proposed approach can be applied not only to the immune safety assessment of the multitude of graphene physical and chemical parameters, but also for graphene applications in neuroscience. Moreover, this approach can be translated to other 2D emerging materials and will likely advance the understanding of their toxicology.     

Sediment phosphate composition in relation to emergent macrophytes in the Doñana Marshes (SW Spain)

We have studied the effect of the presence of emergent macrophytes on the sediment phosphate composition of a eutrophic shallow marsh on the NE margin of Do?ana (SW Spain). Top sediment and water samples were collected from both the open-water and the vegetated sites at three areas covered by different plant species: Scirpus maritimus, Juncus subulatus and Phragmites australis. The concentration of organic matter was significantly higher in the top sediment of sites covered by vegetation than in their adjacent open-water sites at the three vegetation areas. The P-fractional composition showed that the sediment was dominated by the inorganic P-fractions in all cases, reaching the highest concentration in the Ca-bound P-fraction (281-372 microg g(-1) d.w.). The sum of all P-fractions was significantly higher in the top sediment of the sites covered by J. subulatus and S. maritimus than in their adjacent open-water sites, and so were the org-P fraction extracted by hot NaOH and the concentration of phytate within this fraction. Deposition of plant material on the top sediment of areas vegetated by J. subulatus and S. maritimus explains these differences. The P-fractional composition of the seeds from J. subulatus showed that they contained a large proportion of organic P-fractions, particularly of the fraction extracted by hot NaOH (1868 microg g(-1) d.w., 85% of which was phytate). The presence of emergent macrophytes, therefore, influenced the distribution of P-fractions in the sediment depending on plant species. The P-bioavailability of shallow aquatic systems must be fully understood if wetlands are to be protected from further eutrophication.     

Hybridizing Oligonucleotides with Hydrophobic Peptide Nucleic Acids Assists Their Cellular Uptake through Aggregate Formation

We applied hybridization between hydrophobic peptide nucleic acids (PNAs) and oligodeoxynucleotides (ODNs) to achieve their cellular uptake without any need for transfection reagents. We employed a pyrenyl unit as a hydrophobic functional group and introduced it at the terminus of the PNA strand. The pyrene-tethered PNA (PyPNA) strongly bound with its complementary ODNs to generate amphiphiles; the resulting hybrids formed aggregates that showed efficient cellular uptake and high biological stability. Aggregates containing a functional DNA aptamer that bound to the PyPNA penetrated the cell membrane smoothly, with the aptamer exerting its original function in living cells. Thus, PyPNA efficiently assisted the additive-free cellular uptake of ODNs.     

Growth of large-area single- and Bi-layer graphene by controlled carbon precipitation on polycrystalline Ni surfaces

We report graphene films composed mostly of one or two layers of graphene grown by controlled carbon precipitation on the surface of polycrystalline Ni thin films during atmospheric chemical vapor deposition (CVD). Controlling both the methane concentration during CVD and the substrate cooling rate during graphene growth can significantly improve the thickness uniformity. As a result, one- or two- layer graphene regions occupy up to 87% of the film area. Single layer coverage accounts for 5%–11% of the overall film. These regions expand across multiple grain boundaries of the underlying polycrystalline Ni film. The number density of sites with multilayer graphene/graphite (>2 layers) is reduced as the cooling rate decreases. These films can also be transferred to other substrates and their sizes are only limited by the sizes of the Ni film and the CVD chamber. Here, we demonstrate the formation of films as large as 1 in². These findings represent an important step towards the fabrication of large-scale high-quality graphene samples. Electronic Supplementary Material  Supplementary material is available for this article at and is accessible for authorized users.     

Glycosylated Cell-Penetrating Peptides (GCPPs)

The cell membrane regulates the exchange of molecules and information with the external environment. However, this control barrier hinders the delivery of exogenous bioactive molecules that can be applied to correct cellular malfunctions. Therefore, the traffic of macromolecules across the cell membrane represents a great challenge for the development of the next generation of therapies and diagnostic methods. Cell-penetrating peptides are short peptide sequences capable of delivering a broad range of biomacromolecules across the cellular membrane. However, penetrating peptides still suffer from limitations, mainly related to their lack of specificity and potential toxicity. Glycosylation has emerged as a potential promising strategy for the biological improvement of synthetic materials. In this work we have developed a new convergent strategy for the synthesis of penetrating peptides functionalized with glycan residues by an oxime bond connection. The uptake efficiency and intracellular distribution of these glycopeptides have been systematically characterized by means of flow cytometry and confocal microscopy and in zebrafish animal models. The incorporation of these glycan residues into the peptide structure influenced the internalization efficiency and cellular toxicity of the resulting glycopeptide hybrids in the different cell lines tested. The results reported herein highlight the potential of the glycosylation of penetrating peptides to modulate their activity.     

Specific Post-Translational Modifications of VDAC3 in ALS-SOD1 Model Cells Identified by High-Resolution Mass Spectrometry

Damage induced by oxidative stress is a key driver of the selective motor neuron death in amyotrophic lateral sclerosis (ALS). Mitochondria are among the main producers of ROS, but they also suffer particularly from their harmful effects. Voltage-dependent anion-selective channels (VDACs) are the most represented proteins of the outer mitochondrial membrane where they form pores controlling the permeation of metabolites responsible for mitochondrial functions. For these reasons, VDACs contribute to mitochondrial quality control and the entire energy metabolism of the cell. In this work we assessed in an ALS cell model whether disease-related oxidative stress induces post-translational modifications (PTMs) in VDAC3, a member of the VDAC family of outer mitochondrial membrane channel proteins, known for its role in redox signaling. At this end, protein samples enriched in VDACs were prepared from mitochondria of an ALS model cell line, NSC34 expressing human SOD1G93A, and analyzed by nUHPLC/High-Resolution nESI-MS/MS. Specific over-oxidation, deamidation, succination events were found in VDAC3 from ALS-related NSC34-SOD1G93A but not in non-ALS cell lines. Additionally, we report evidence that some PTMs may affect VDAC3 functionality. In particular, deamidation of Asn215 alone alters single channel behavior in artificial membranes. Overall, our results suggest modifications of VDAC3 that can impact its protective role against ROS, which is particularly important in the ALS context. Data are available via ProteomeXchange with identifier PXD036728.