ddRAD Sequencing and DNA Barcoding.

Double-digest restriction site-associated DNA sequencing is a library preparation protocol that enables capturing variable sites across the genome including single-nucleotide polymorphisms (SNPs). These SNPs can be utilized to gain evolutionary insights into patterns observed in DNA barcodes, to infer population structure and phylogenies, to detect gene flow and introgression, and to perform species delimitation analyses. The protocol includes chemically shearing genomic DNA with restriction enzymes, unique tagging, size selection, and amplification of the resulting DNA fragments.

Magnetic behavior and ground spin states for coordination {L·[M(Hal)]} assemblies (Hal = Cl or I) of radical trianion hexacyanohexaazatriphenylenes (L) with three coordinated high-spin Fe ( = 2) or Co ( = 3/2) centers.

A series of trianion assemblies of hexaazatriphenylenehexacarbonitrile {HAT(CN)} and hexaazatrinaphthylenehexacarbonitrile {HATNA(CN)} with three Fe(II) or Co(II) ions: {cryptand(K)}·{HATNA(CN)·(FeI)}·2CHCl (1), {cryptand(K)}·{HATNA(CN)·(CoI)}·2CHCl (2), and (CV)·{HAT(CN)·(CoCl)}·0.5(CVCl)·2.5CHCl (3) are synthesized (CVCl = crystal violet).

Enhancing the Performance of the Photonic Integrated Sensing System by Applying Frequency Interrogation.

Lab-on-a-chip systems are currently one of the most promising areas in the development of ultra-compact sensor systems, used primarily for gas and liquid analysis to determine the concentration of impurities. Integrated photonics is an ideal basis for designing "lab-on-a-chip" systems, advantageous for its compactness, energy efficiency, and low cost in mass production. This paper presents a solution for "lab-on-a-chip" device realization, consisting of a sensor and an interrogator based on a silicon-on-insulator (SOI) integrated photonics platform.

Design and Modeling of a Fully Integrated Microring-Based Photonic Sensing System for Liquid Refractometry.

The design of a refractometric sensing system for liquids analysis with a sensor and the scheme for its intensity interrogation combined on a single photonic integrated circuit (PIC) is proposed. A racetrack microring resonator with a channel for the analyzed liquid formed on the top is used as a sensor, and another microring resonator with a lower Q-factor is utilized to detect the change in the resonant wavelength of the sensor. As a measurement result, the optical power at its drop port is detected in comparison with the sum of the powers at the through and drop ports.

Design of an electron cyclotron emission diagnostics suite for COMPASS Upgrade tokamak.

COMPASS Upgrade is a medium size and high field tokamak that is capable of addressing key challenges for reactor grade tokamaks, including power exhaust and advanced confinement scenarios. Electron cyclotron emission will be available among the first diagnostics to provide measurements of high spatial and temporal resolution of electron temperature profiles and electron temperature fluctuation profiles through a radial view. A separate oblique view at 12° from normal will be utilized to study non-thermal electrons.

The effect of hypochlorite- and peroxide-induced oxidation of plasminogen on damage to the structure and biological activity.

In this study, we examined for the first time the effect of the HOCl/OCl- and HO-induced oxidation of Glu-plasminogen on damage to its primary structure and the biological activity of plasmin. The consolidated results obtained with the aid of MS/MS, electrophoresis, and colourimetry, demonstrated that none of the oxidised amino acid residues found in the proenzyme treated with 25 μM HOCl/OCl or 100 μM HO were functionally significant for plasminogen. However, the treatment of plasminogen with increasing concentrations of HOCl/OCl from 25 μM to 100 μM or HO from 100 μM to 300 μM promoted a partial loss in the activity of oxidised plasmin.

A molecular-based identification resource for the arthropods of Finland.

To associate specimens identified by molecular characters to other biological knowledge, we need reference sequences annotated by Linnaean taxonomy. In this study, we (1) report the creation of a comprehensive reference library of DNA barcodes for the arthropods of an entire country (Finland), (2) publish this library, and (3) deliver a new identification tool for insects and spiders, as based on this resource. The reference library contains mtDNA COI barcodes for 11,275 (43%) of 26,437 arthropod species known from Finland, including 10,811 (45%) of 23,956 insect species.

Relevance of ddRADseq method for species and population delimitation of closely related and widely distributed wolf spiders (Araneae, Lycosidae).

Although species delimitation is often controversial, emerging DNA-based and classical morphology-based methods are rarely compared using large-scale samplings, even less in the case of widely distributed species that have distant, allopatric populations. In the current study, we examined species boundaries within two wolf spider species of the genus Pardosa (Araneae, Lycosidae), P. riparia and P.

Adsorption of proteins on gold nanoparticles: One or more layers?

Adsorption of proteins on nanoparticles is a complex and poorly studied process. The mechanisms of protein layer formation can fundamentally differ depending on the composition of the medium, the nanoparticles' structure, the protein's nature, and other factors. In particular, monolayer or multilayer immobilization may occur.

Information Dropout Patterns in Restriction Site Associated DNA Phylogenomics and a Comparison with Multilocus Sanger Data in a Species-Rich Moth Genus.

A rapid shift from traditional Sanger sequencing-based molecular methods to the phylogenomic approach with large numbers of loci is underway. Among phylogenomic methods, restriction site associated DNA (RAD) sequencing approaches have gained much attention as they enable rapid generation of up to thousands of loci randomly scattered across the genome and are suitable for nonmodel species. RAD data sets however suffer from large amounts of missing data and rapid locus dropout along with decreasing relatedness among taxa.

Mitonuclear discordance in wolf spiders: Genomic evidence for species integrity and introgression.

Systematists and taxonomists have benefited greatly from the emergence of molecular methods. Species identification has become straightforward through DNA barcoding and the rapid build-up of massive DNA barcode reference libraries. In animals, mitonuclear discordance can significantly complicate the process of species identification and delimitation.