Due to bandwidth limitations of state of the art electronics, the transient transport properties of molecular junctions are experimentally a terra incognita, which can only be explored if novel picosecond current-probing techniques are developed. Here we demonstrate one such approach: the laser pulse-pair sequence scheme. The method is used to monitor in picosecond resolution the oxidation state of a redox molecule, 6-ferrocenyl-1-hexanethiol, within a junction and to quantify its redox rate constant, which is found to be (80 ps)⁻¹.

Irys Extract is a software tool for generating genomic information from data collected by the BioNano Genomics Irys platform. The tool allows the user easy access to the raw data in the form of cropped images and genetically aligned intensity profiles. The latter are also made compatible with the BED format for using with popular genomic browsers such as the UCSC Genome Browser. Irys Extract has been developed in Matlab R2015a, it was tested to work with IrysView 2.4.0.15879 and AutoDetect 2.1.4.9159, and it currently runs under Microsoft Windows operating systems (7-10). Irys Extract can be downloaded alongside its manual and a demo dataset at http://www.nanobiophotonix.com and https://sites.google.com/site/raniarielly/. Supplementary data are available at Bioinformatics online.

The epigenetic mark 5-hydroxymethylcytosine (5-hmC) is a distinct product of active enzymatic demethylation that is linked to gene regulation, development and disease. Genome-wide 5-hmC profiles generated by short-read next-generation sequencing are limited in providing long-range epigenetic information relevant to highly variable genomic regions, such as the 3.7 Mbp disease-related Human Leukocyte Antigen (HLA) region. We present a long-read, single-molecule mapping technology that generates hybrid genetic/epigenetic profiles of native chromosomal DNA. The genome-wide distribution of 5- hmC in human peripheral blood cells correlates well with 5-hmC DNA immunoprecipitation (hMeDIP) sequencing. However, the long read length of 100 kbp-1Mbp produces 5-hmC profiles across variable genomic regions that failed to showup in the sequencing data. In addition, optical 5-hmC mapping shows strong correlation between the 5-hmC density in gene bodies and the corresponding level of gene expression. The single molecule concept provides information on the distribution and coexistence of 5-hmC signals at multiple genomic loci on the same genomic DNA molecule, revealing long-range correlations and cell-to-cell epigenetic variation.

Detection of hazardous gases and vapors, that may be lethal in minute doses, requires sensitive detector. A timely warning, preferably before gas exceed a predetermined threshold, depends on the capability to map the gas concentration inside a complex structure. That requires a constant spatial monitoring of gas concentrations at various locations. This work presents a generic pooling approach for spatial gas concentration mapping using a single detector. It is based on gas collection from several points simultaneously at predetermined mixing ratios. The gas concentration at each sampling point (SP) is computed using a repetitious scheme, based on the sensor readings and the mixing ratios.

Identification of chemical properties in the inner tissues of fresh produce would enable us to identify major issues plaguing the agriculture supply chain, like off-flavors and core rot since these are caused by or accompanied by known chemical elements. We show the development of transmission Raman spectroscopy system for identifying these elements by addressing several issues: we located an optimal spectral window by conducting optical attenuation measurements and calculated the required LASER power in that range. For apple tissues, this optical window was found in the 700–950 nm range, and the required LASER power range was calculated to be in the 40–700 mW range. We also calculated that the optimal shifted-excitation Raman difference spectroscopy wavelengths should be separated by 0.7 nm in order to optimally produce narrow and high-intensity Raman peak features and eliminate the competing fluorescence signal. Finally, we provide a complete optical system design with exact optimal parameters. In contrast to other fields like pharmaceuticals and medicine, transmission Raman spectroscopy has not been applied extensively in agriculture. Therefore, this study fills a gap in that field’s applicability.