Ra isotope perspective on the hydrology and continuity of permafrost in the high Arctic.

The continuous permafrost in the valleys of Svalbard is dotted by pingos, which are small hills formed by the near surface freezing of ascending groundwater. In this study, we used H and Ra isotopes to inquire into the sub-surface residence time of groundwater discharging at these pingos. While its low H suggests that the pingo-associated groundwater is basically not modern (i.

Ag-Mediated Folding of Long Polyguanine Strands to Double and Quadruple Helixes.

Metal-mediated base pairing of DNA has been a topic of extensive research spanning over more than four decades. Precise positioning of a single metal ion by predetermining the DNA sequence, as well as improved conductivity offered by the ions, make these structures interesting candidates in the context of using DNA in nanotechnology. Here, we report the formation and characterization of conjugates of long (kilo bases) homoguanine DNA strands with silver ions.

FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA.

Analysis of DNA methylation in cell-free DNA reveals clinically relevant biomarkers but requires specialized protocols such as whole-genome bisulfite sequencing. Meanwhile, millions of cell-free DNA samples are being profiled by whole-genome sequencing. Here, we develop FinaleMe, a non-homogeneous Hidden Markov Model, to predict DNA methylation of cell-free DNA and, therefore, tissues-of-origin, directly from plasma whole-genome sequencing.

Liquid biopsy detection of genomic alterations in pediatric brain tumors from cell-free DNA in peripheral blood, CSF, and urine.

Background: The ability to identify genetic alterations in cancers is essential for precision medicine; however, surgical approaches to obtain brain tumor tissue are invasive. Profiling circulating tumor DNA (ctDNA) in liquid biopsies has emerged as a promising approach to avoid invasive procedures. Here, we systematically evaluated the feasibility of profiling pediatric brain tumors using ctDNA obtained from plasma, cerebrospinal fluid (CSF), and urine.

Electronic Level Structure of Novel Guanine Octuplex DNA Single Molecules.

Throughout the past few decades, guanine quadruplex DNA structures have attracted much interest both from a fundamental material science perspective and from a technologically oriented perspective. Novel guanine octuplex DNA, formed from coiled quadruplex DNA, was recently discovered as a stable and rigid DNA-based nanostructure. A detailed electronic structure study of this new nanomaterial, performed by scanning tunneling spectroscopy on a subsingle-molecule level at cryogenic temperature, is presented herein.

Formation of Novel Octuplex DNA Molecules from Guanine Quadruplexes.

Guanine quadruplex (G4)-DNA structures have sparked the interest of many scientists due to their important biological roles and their potential use in molecular nanoelectronics and nanotechnology. The high guanine content in G4-DNA endows it with mechanical stability, robustness, and improved charge transport properties-attractive attributes for a molecular nanowire. The self-driven formation of a novel G4-DNA-based nanostructure, coined guanine octuplex (G8)-DNA, is reported herein.

Direct monitoring of the stepwise condensation of kinetoplast DNA networks.

Condensation and remodeling of nuclear genomes play an essential role in the regulation of gene expression and replication. Yet, our understanding of these processes and their regulatory role in other DNA-containing organelles, has been limited. This study focuses on the packaging of kinetoplast DNA (kDNA), the mitochondrial genome of kinetoplastids.

Backbone charge transport in double-stranded DNA.

Understanding charge transport in DNA molecules is a long-standing problem of fundamental importance across disciplines. It is also of great technological interest due to DNA's ability to form versatile and complex programmable structures. Charge transport in DNA-based junctions has been reported using a wide variety of set-ups, but experiments so far have yielded seemingly contradictory results that range from insulating or semiconducting to metallic-like behaviour.

Genome-wide cell-free DNA mutational integration enables ultra-sensitive cancer monitoring.

In many areas of oncology, we lack sensitive tools to track low-burden disease. Although cell-free DNA (cfDNA) shows promise in detecting cancer mutations, we found that the combination of low tumor fraction (TF) and limited number of DNA fragments restricts low-disease-burden monitoring through the prevailing deep targeted sequencing paradigm. We reasoned that breadth may supplant depth of sequencing to overcome the barrier of cfDNA abundance.

Electronic Level Structure of Silver-Intercalated Cytosine Nanowires.

Metal-mediated base-paired DNA has long been investigated for basic scientific pursuit and for nanoelectronics purposes. Particularly attractive in these domains is the Ag-intercalated polycytosine DNA duplex. Extensive studies of this molecule have led to our current understanding of its self-assembly properties, high thermodynamic and structural stability, and high longitudinal conductivity.

Sensitive Detection of Minimal Residual Disease in Patients Treated for Early-Stage Breast Cancer.

Purpose: Existing cell-free DNA (cfDNA) methods lack the sensitivity needed for detecting minimal residual disease (MRD) following therapy. We developed a test for tracking hundreds of patient-specific mutations to detect MRD with a 1,000-fold lower error rate than conventional sequencing.

Experimental Design: We compared the sensitivity of our approach to digital droplet PCR (ddPCR) in a dilution series, then retrospectively identified two cohorts of patients who had undergone prospective plasma sampling and clinical data collection: 16 patients with ER+/HER2- metastatic breast cancer (MBC) sampled within 6 months following metastatic diagnosis and 142 patients with stage 0 to III breast cancer who received curative-intent treatment with most sampled at surgery and 1 year postoperative.

Durable, Stable, and Functional Nanopores Decorated by Self-Assembled Dipeptides.

Nanopores have become an important tool for the detection and analysis of molecules at the single-molecule level. Surface modification of solid-state nanopores can improve their durability and efficiency. Peptides are ideal for surface modifications as they allow tailoring of multiple properties by a rational design of their sequence.

Electrical Characterization of Individual Cesium Lead Halide Perovskite Nanowires Using Conductive AFM.

Perovskite nanostructures have attracted much attention in recent years due to their suitability for a variety of applications such as photovoltaics, light-emitting diodes (LEDs), nanometer-size lasing, and more. These uses rely on the conductive properties of these nanostructures. However, electrical characterization of individual, thin perovskite nanowires has not yet been reported.

Temperature Dependence of the STM Morphology and Electronic Level Structure of Silver-Containing DNA.

Understanding the effect of external conditions, temperature in particular, on novel nanomaterials is of great significance. The powerful ability of scanning tunneling microscopy (STM) to characterize topography and electronic levels on a single molecule scale is utilized herein to characterize individual silver-containing poly(dG)-poly(dC) DNA molecules, at different temperatures. These measurements indicate that the molecule is a truly hybrid metal-organic nanomaterial with electronic states originating from both the DNA and the embedded silver.

Scanning Tunneling Microscopy and Spectroscopy of Novel Silver-Containing DNA Molecules.

The quest for a suitable molecule to pave the way to molecular nanoelectronics has been met with obstacles for over a decade. Candidate molecules such as carbon nanotubes lack the appealing trait of self-assembly, while DNA seems to lack the desirable feature of conductivity. Silver-containing poly(dG)-poly(dC) DNA (E-DNA) molecules have recently been reported as promising candidates for molecular electronics, owing to the selectivity of their metallization, their thin and uniform structure, their resistance to deformation, and their maximum possible high conductivity.

Single Domain 10 nm Ferromagnetism Imprinted on Superparamagnetic Nanoparticles Using Chiral Molecules.

The rapid growth in demand for data and the emerging applications of Big Data require the increase of memory capacity. Magnetic memory devices are among the leading technologies for meeting this demand; however, they rely on the use of ferromagnets that creates size reduction limitations and poses complex materials requirements. Usually magnetic memory sizes are limited to 30-50 nm.

Crystallographic orientation errors in mechanical exfoliation.

We evaluate the effect of mechanical exfoliation of van der Waals materials on crystallographic orientations of the resulting flakes. Flakes originating from a single crystal of graphite, whose orientation is confirmed using STM, are studied using facet orientations and electron back-scatter diffraction (EBSD). While facets exhibit a wide distribution of angles after a single round of exfoliation ([Formula: see text]), EBSD shows that the true crystallographic orientations are more narrowly distributed ([Formula: see text]), and facets have an approximately [Formula: see text] error from the true orientation.

Tumor fraction in cell-free DNA as a biomarker in prostate cancer.

Background: Tumor content in circulating cell-free DNA (cfDNA) is a promising biomarker, but longitudinal dynamics of tumor-derived and non-tumor-derived cfDNA through multiple courses of therapy have not been well described.

Methods: CfDNA from 663 plasma samples from 140 patients with castration-resistant prostate cancer (CRPC) was subject to sparse whole genome sequencing. Tumor fraction (TFx) estimated using the computational tool ichorCNA was correlated with clinical features and responses to therapy.

Advances in Synthesis and Measurement of Charge Transport in DNA-Based Derivatives.

Charge transport through molecular structures is interesting both scientifically and technologically. To date, DNA is the only type of polymer that transports significant currents over distances of more than a few nanometers in individual molecules. For molecular electronics, DNA derivatives are by far more promising than native DNA due to their improved charge-transport properties.

Structural Alterations Driving Castration-Resistant Prostate Cancer Revealed by Linked-Read Genome Sequencing.

Nearly all prostate cancer deaths are from metastatic castration-resistant prostate cancer (mCRPC), but there have been few whole-genome sequencing (WGS) studies of this disease state. We performed linked-read WGS on 23 mCRPC biopsy specimens and analyzed cell-free DNA sequencing data from 86 patients with mCRPC. In addition to frequent rearrangements affecting known prostate cancer genes, we observed complex rearrangements of the AR locus in most cases.

Highly Conductive Thin Uniform Gold-Coated DNA Nanowires.

Over the past decades, DNA, the carrier of genetic information, has been used by researchers as a structural template material. Watson-Crick base pairing enables the formation of complex 2D and 3D structures from DNA through self-assembly. Various methods have been developed to functionalize these structures for numerous utilities.