Analytical validation of NeXT Personal®, an ultra-sensitive personalized circulating tumor DNA assay.

We describe the analytical validation of NeXT Personal®, an ultra-sensitive, tumor-informed circulating tumor DNA (ctDNA) assay for detecting residual disease, monitoring therapy response, and detecting recurrence in patients diagnosed with solid tumor cancers. NeXT Personal uses whole genome sequencing of tumor and matched normal samples combined with advanced analytics to accurately identify up to ~1,800 somatic variants specific to the patient's tumor. A personalized panel is created, targeting these variants and then used to sequence cell-free DNA extracted from patient plasma samples for ultra-sensitive detection of ctDNA. The NeXT Personal analytical validation is based on panels designed from tumor and matched normal samples from two cell lines, and from 123 patients across nine cancer types. Analytical measurements demonstrated a detection threshold of 1.67 parts per million (PPM) with a limit of detection at 95% (LOD95) of 3.45 PPM. NeXT Personal showed linearity over a range of 0.8 to 300,000 PPM (Pearson correlation coefficient = 0.9998). Precision varied from a coefficient of variation of 12.8% to 3.6% over a range of 25 to 25,000 PPM. The assay targets 99.9% specificity, with this validation study measuring 100% specificity and in silico methods giving us a confidence interval of 99.92 to 100%. In summary, this study demonstrates NeXT Personal as an ultra-sensitive, highly quantitative and robust ctDNA assay that can be used to detect residual disease, monitor treatment response, and detect recurrence in patients.

The Impact of Optical Berry Sorting on Red Wine Composition and Sensory Properties.

The impact of optical berry sorting was investigated using Grenache, Barbera, and Cabernet Sauvignon grapes from Yolo County, California in 2016. Optical sorting parameters were adjusted to remove underripe berries and material other than grapes using color parameters. Wines were made from three treatments, control (no sorting), sort (accepted material), and reject (material rejected by the optical sorter). The rate of rejection was approximately 14.9%, 3.9%, and 1.5% (w/w) for Grenache, Barbera, and Cabernet Sauvignon, respectively. Chemical composition in the finished wines was analyzed by the Adams-Harbertson assay and reversed-phase high-performance liquid chromatography for phenolics, and head-space solid-phase microextraction gas chromatography mass spectrometry for aroma profiling. In general, optical sorting was successful in removing underripe berries and material other than grapes as evidenced by lower ethanol levels and higher concentrations of total phenolics and tannin (due to the inclusion of material other than grapes) in wine made from rejected material. Despite this, no difference in final ethanol content and minimal differences in phenolic composition were observed between control and sort treatment wines for the three varieties studied. Differences were observed in the aroma profiles of the reject treatments for all three varieties compared to sort and control; however, few compounds differed significantly between the sort and control treatments. Descriptive sensory analysis revealed that panelists had difficulty distinguishing aroma, taste, mouthfeel, and color parameters among wines made from different treatments for all three varieties. Thus, optical sorting had minimal impact on wine sensory properties using the varieties and vineyards studied. Optical sorting may be used to differentiate and sort for different ripeness levels using color as a primary criterion; however, the impact on the resulting wine is likely dependent on the initial variability in grape ripeness.

Impact of grapevine red blotch disease on primary and secondary metabolites in 'Cabernet Sauvignon' grape tissues.

The grapevine red blotch disease (GRBD) was first noticed in 2008, impacting grape ripening. In general, GRBD reduces grape and wine quality resulting in significant economic losses. The purpose of the present study was to evaluate the effect of GRBD on agronomical parameters of 'Cabernet Sauvignon' vines at harvest. Using a metabolomics approach, the influence on primary and secondary metabolite profiling in skin + pulp/flesh and seeds were also determined. GRBD influenced °Brix and berry weight, as well as primary and secondary metabolites in both tissues. 1D 1H NMR was effective in quantifying the main primary and secondary metabolites affected by GRBD. RP-HPLC was similarly able to quantify the main phenolics affected. Multivariate analysis showed the influence of the virus on grape metabolites using both tools in two berry tissues. The effectiveness of both tools to describe sample variability was compared and the most affected metabolites in each tissue could be identified.

Trunk Girdling Increased Stomatal Conductance in Cabernet Sauvignon Grapevines, Reduced Glutamine, and Increased Malvidin-3-Glucoside and Quercetin-3-Glucoside Concentrations in Skins and Pulp at Harvest.

Girdling is a traditional horticultural practice applied at fruit set or other phenological stages, and is used mostly as a vine management. In grapevines, it is used primarily for table grapes to improve berry weight, sugar content, color, and to promote early harvest. The objective of this study was to evaluate the effect of trunk girdling applied at veraison, in 'Cabernet Sauvignon' wine grapes (Vitis vinifera L.), on agronomical and physiological parameters during vine development from the onset of ripening (veraison) to harvest, and additionally to quantify the effect of girdling on primary and secondary metabolism. Girdling was applied 146 days after pruning (dap) at veraison, when berry sampling for metabolomics and agronomical evaluations commenced, with a further three sampling dates until harvest, at 156 dap (30% maturation, 10 days after girdling-dag), 181 dap (70% maturation, 35 dag), and 223 dap (commercial harvest, 77 dag). Skin/pulp and seed tissues were extracted separately and metabolomics was performed using one-dimensional proton nuclear magnetic resonance (1D 1H NMR) spectroscopy and high performance liquid chromatography (HPLC-DAD). At harvest, girdling significantly increased stomatal conductance (gs) in vines, decreased glutamine concentrations, and increased anthocyanin and flavonol concentrations in the skin/pulp tissues of grape berries. Berry weight was reduced by 27% from 181 dap to harvest, and was significantly higher in grapes from girdled vines at 181 dap. Sugars, organic acids, and other amino acids in skin/pulp or seeds were not significantly different, possibly due to extra-fascicular phloem vessels transporting metabolites from leaves to the roots. Using a metabolomics approach, differences between skin/pulp and seeds tissues were meaningful, and a greater number of secondary metabolites in skin/pulp was affected by girdling than in seeds. Girdling is a simple technique that could easily be applied commercially on vine management to improve berry color and other phenolics in 'Cabernet Sauvignon' grapes.

Quantum capacitance-limited MoS2 biosensors enable remote label-free enzyme measurements.

We have demonstrated atomically thin, quantum capacitance-limited, field-effect transistors (FETs) that enable the detection of pH changes with 75-fold higher sensitivity (≈4.4 V per pH) over the Nernst value of 59 mV per pH at room temperature when used as a biosensor. The transistors, which are fabricated from monolayer films of MoS2, use a room temperature ionic liquid (RTIL) in place of a conventional oxide gate dielectric and exhibit very low intrinsic noise resulting in a pH resolution of 92 × 10-6 at 10 Hz. This high device performance, which is a function of the structure of our device, is achieved by remotely connecting the gate to a pH sensing element allowing the FETs to be reused. Because pH measurements are fundamentally important in biotechnology, the increased resolution demonstrated here will benefit numerous applications ranging from pharmaceutical manufacturing to clinical diagnostics. As an example, we experimentally quantified the function of the kinase Cdk5, an enzyme implicated in Alzheimer's disease, at concentrations that are 5-fold lower than physiological values, and with sufficient time-resolution to allow the estimation of both steady-state and kinetic parameters in a single experiment. The high sensitivity, increased resolution, and fast turnaround time of the measurements will allow the development of early diagnostic tools and novel therapeutics to detect and treat neurological conditions years before currently possible.

Impact of Grapevine Red Blotch Disease on Grape Composition of Vitis vinifera Cabernet Sauvignon, Merlot, and Chardonnay.

Grapevine red blotch disease (GRBD) is a recently recognized viral disease that affects grapevines ( Vitis vinifera L.). Currently little is known about its impact on grape composition. This study focused on the impact of GRBD on grape primary and secondary metabolites (mainly phenolic compounds) of three Vitis vinifera L. cultivars during two seasons. Grapes from symptomatic red blotch diseased vines (RB (+)) mostly had lower concentration of total soluble solids (TSS) and higher titratable acidity (TA) levels when compared to grapes from healthy vines (RB (-)) at harvest. GRBD impacted grape phenolic composition by mostly decreasing anthocyanin and increasing flavonol and proanthocyanidin (PA) contents in berry skins. No major impacts were observed on seed phenolics. RB (+) grapes contained more amino and carboxylic acids, while RB (-) grapes contained more oligosaccharides, polyols, and some specific monosaccharides at harvest. The impact of GRBD on grape composition was variable and dependent on the cultivar, site, and season.

Valence Band Dependent Charge Transport in Bulk Molecular Electronic Devices Incorporating Highly Conjugated Multi-[(Porphinato)Metal] Oligomers.

Molecular electronics offers the potential to control device functions through the fundamental electronic properties of individual molecules, but realization of such possibilities is typically frustrated when such specialized molecules are integrated into a larger area device. Here we utilize highly conjugated (porphinato)metal-based oligomers (PM(n) structures) as molecular wire components of nanotransfer printed (nTP) molecular junctions; electrical characterization of these "bulk" nTP devices highlights device resistances that depend on PM(n) wire length. Device resistance measurements, determined as a function of PM(n) molecular length, were utilized to evaluate the magnitude of a phenomenological ß corresponding to the resistance decay parameter across the barrier; these data show that the magnitude of this ß value is modulated via porphyrin macrocycle central metal atom substitution [ß(PZn(n); 0.065 Å(-1)) < ß(PCu(n); 0.132 Å(-1)) < ß(PNi(n); 0.176 Å(-1))]. Cyclic voltammetric data, and ultraviolet photoelectron spectroscopic studies carried out at gold surfaces, demonstrate that these nTP device resistances track with the valence band energy levels of the PM(n) wire, which were modulated via porphyrin macrocycle central metal atom substitution. This study demonstrates the ability to fabricate "bulk" and scalable electronic devices in which function derives from the electronic properties of discrete single molecules, and underscores how a critical device function--wire resistance--may be straightforwardly engineered by PM(n) molecular composition.

Iron(II) spin crossover films on Au(111): scanning probe microscopy and photoelectron spectroscopy.

The growth of films of [H2B(pz)2]Fe(ii)(bpy) on Au(111) is characterized from the bilayer film to multilayer film regime. Scanning tunneling microscopy shows a transition from a well-ordered, uniform bilayer film to a poorly-ordered film at larger thicknesses. Previous local tunneling spectroscopy and conductance mapping in bilayer films permit the identification of coexisting molecular spin-states at all temperatures. New ultraviolet photoelectron spectroscopy is consistent with this picture and in agreement with the density of states calculated by density functional theory. In thicker films with a polycrystalline morphology, evidence for a more bulk-like change in spin composition as a function of temperature is obtained by observing the reduction in intensity of Fe 2p core level satellites in X-ray photoelectron spectra.

Tunneling characteristics of Au-alkanedithiol-Au junctions formed via nanotransfer printing (nTP).

Construction of permanent metal-molecule-metal (MMM) junctions, though technically challenging, is desirable for both fundamental investigations and applications of molecule-based electronics. In this study, we employed the nanotransfer printing (nTP) technique using perfluoropolyether (PFPE) stamps to print Au thin films onto self-assembled monolayers (SAMs) of alkanedithiol formed on Au thin films. We show that the resulting MMM junctions form permanent and symmetrical tunnel junctions, without the need for an additional protection layer between the top metal electrode and the molecular layer. This type of junction makes it possible for direct investigations into the electrical properties of the molecules and the metal-molecule interfaces. Dependence of transport properties on the length of the alkane molecules and the area of the printed Au electrodes has been examined systematically. From the analysis of the current-voltage (I-V) curves using the Simmons model, the height of tunneling barrier associated with the molecule (alkane) has been determined to be 3.5 ± 0.2 eV, while the analysis yielded an upper bound of 2.4 eV for the counterpart at the interface (thiol). The former is consistent with the theoretical value of ~3.5-5.0 eV. The measured I-V curves show scaling with respect to the printed Au electrode area with lateral dimensions ranging from 80 nm to 7 µm. These results demonstrate that PFPE-assisted nTP is a promising technique for producing potentially scalable and permanent MMM junctions. They also demonstrate that MMM structures (produced by the unique PFPE-assisted nTP) constitute a reliable test bed for exploring molecule-based electronics.