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. Simulations showed the possibility of registering a change in the analyte refractive index with a sensitivity of 110 nm per refractive index unit. The proposed scheme was analyzed with a broadband source, as well as a source based on an optoelectronic oscillator using an optical phase modulator. The second case showed the fundamental possibility of implementing an intensity interrogator on a PIC using an external typical single-mode laser as a source. Meanwhile, additional simulations demonstrated an increased system sensitivity compared to the conventional interrogation scheme with a broadband or tunable light source. The proposed approach provides the opportunity to increase the integration level of a sensing device, significantly reducing its cost, power consumption, and dimensions.

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. The relationship between locus dropout and the amount of phylogenetic information retained in the data has remained largely uninvestigated. Similarly, phylogenetic hypotheses based on RAD have rarely been compared with phylogenetic hypotheses based on multilocus Sanger sequencing, even less so using exactly the same species and specimens. We compared the Sanger-based phylogenetic hypothesis (8 loci; 6172 bp) of 32 species of the diverse moth genus Eupithecia (Lepidoptera, Geometridae) to that based on double-digest RAD sequencing (3256 loci; 726,658 bp). We observed that topologies were largely congruent, with some notable exceptions that we discuss. The locus dropout effect was strong. We demonstrate that number of loci is not a precise measure of phylogenetic information since the number of single-nucleotide polymorphisms (SNPs) may remain low at very shallow phylogenetic levels despite large numbers of loci. As we hypothesize, the number of SNPs and parsimony informative SNPs (PIS) is low at shallow phylogenetic levels, peaks at intermediate levels and, thereafter, declines again at the deepest levels as a result of decay of available loci. Similarly, we demonstrate with empirical data that the locus dropout affects the type of loci retained, the loci found in many species tending to show lower interspecific distances than those shared among fewer species. We also examine the effects of the numbers of loci, SNPs, and PIS on nodal bootstrap support, but could not demonstrate with our data our expectation of a positive correlation between them. We conclude that RAD methods provide a powerful tool for phylogenomics at an intermediate phylogenetic level as indicated by its broad congruence with an eight-gene Sanger data set in a genus of moths. When assessing the quality of the data for phylogenetic inference, the focus should be on the distribution and number of SNPs and PIS rather than on loci.

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. The causes of mitonuclear discordance are either biological (e.g., introgression, incomplete lineage sorting, horizontal gene transfer androgenesis) or induced by operational factors (e.g., human error with specimen misidentification or incorrect species delimitation). Moreover, endosymbionts may play an important role in promoting fixation of mitochondrial genomes. Here, we study the mitonuclear discordance of wolf spiders species (Lycosidae) (independent cases from Alopecosa aculeata and Pardosa pullata groups) that share identical COI DNA barcodes. We approached the case utilizing double-digest restriction site-associated DNA sequencing (ddRADseq) to obtain and analyse genomic-scale data. Our results suggest that the observed cases of mitonuclear discordance are not due to operational reasons but result from biological processes. Further analysis indicated introgression and that incomplete lineage sorting is unlikely to have been responsible for the observed discrepancy. Additional survey of endosymbionts provided ideas on further research and their role in shaping mitochondrial DNA distribution patterns. Thus, ddRADseq grants an efficient way to study the taxonomy of problematic groups with insight into underlying evolutionary processes.

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. Here we provide a detailed description of each step of the protocol, as well as information on essential equipment and common issues encountered during laboratory work.

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

A series of trianion assemblies of hexaazatriphenylenehexacarbonitrile {HAT(CN)6} and hexaazatrinaphthylenehexacarbonitrile {HATNA(CN)6} with three Fe(II) or Co(II) ions: {cryptand(K+)}3·{HATNA(CN)6·(FeIII2)3}3-·2C6H4Cl2 (1), {cryptand(K+)}3·{HATNA(CN)6·(CoIII2)3}3-·2C6H4Cl2 (2), and (CV+)3·{HAT(CN)6·(CoIICl2)3}3-·0.5(CVCl)·2.5C6H4Cl2 (3) are synthesized (CVCl = crystal violet). Salt 1 has a χMT value of 9.80 emu K mol-1 at 300 K, indicating a contribution of three high-spin FeII (S = 2) and one S = 1/2 of HATNA(CN)6˙3-. The χMT value increases with cooling up to 12.92 emu K mol-1 at 28 K, providing a positive Weiss temperature of +20 K. Such behavior is described using a strong antiferromagnetic coupling between S = 2 and S = 1/2 with J1 = -82.1 cm-1 and a weaker FeII-FeII antiferromagnetic coupling with J2 = -7.0 cm-1. As a result, the spins of three Fe(II) ions (S = 2) align parallel to each other forming a high-spin S = 11/2 system. Density functional theory (DFT) calculations support a high-spin state of CoII (S = 3/2) for 2 and 3. However, the χMT value of 2 and 3 is 2.25 emu K mol-1 at 300 K, which is smaller than 6 emu K mol-1 calculated for the system with three independent S = 3/2 and one S = 1/2 spins. In contrast to 1, the χMT values decrease with cooling to 0.13-0.36 emu K mol-1 at 1.9 K, indicating that spins of cobalt atoms align antiparallel to each other. Data fitting using PHI software for the model consisting of three high-spin Co(II) ions and an S = 1/2 radical ligand shows very large CoII-L˙3- coupling for 2 and 3 with J1 values of -442 and -349 cm-1. The CoII-CoII coupling via the ligand (J2) is also large, being -100 and -84 cm-1, respectively, which is more than 10 times larger than that of 1. One of the reasons for the J2 increase may be the shortening of the Co-N(L) bonds in 3 and 2 to 2.02(2) and 1.993(12) Å. DFT calculations support the population of the quartet state for the Co3 system, whereas the high-spin decet (S = 9/2) state is positioned higher by 680 cm-1 and is not populated at 300 K. This is explained by the large CoII-CoII coupling. Thus, a balance between J1 and J2 couplings provides parallel or antiparallel alignment of the FeII and CoII spins, leading to high- or low-spin ground states of {L·[MII(Hal)2]3}3-.

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. The sensor function is performed by an all-pass microring resonator (MRR), installed as a notch filter in the feedback circuit of an optoelectronic oscillator based on an electro-optic phase modulator. This structure realizes the frequency interrogation of the sensor with high accuracy and speed using a conventional single-mode laser source. The system sensitivity for the considered gases is 13,000 GHz/RIU. The results show that the use of frequency interrogation makes it possible to increase the intrinsic LoD by five orders. The proposed solution opens an opportunity for fully integrated implementation of a photonic "laboratory-on-a-chip" unit.

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 H2O2-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 H2O2 were functionally significant for plasminogen. However, the treatment of plasminogen with increasing concentrations of HOCl/OCl- from 25 µM to 100 µM or H2O2 from 100 µM to 300 µM promoted a partial loss in the activity of oxidised plasmin. Several methionine residues (Met57, Met182, Met385, Met404, Met585, and Met788) localized in different protein domains have been shown to serve as ROS traps, thus providing an efficient defense mechanism against oxidative stress. Oxidised Trp235, Trp417, Trp427, Trp761, and Tyr672 are most likely responsible for the reduced biological activity of Glu-plasminogen subjected to strong oxidation. The results of the present study, along with those of previous studies, indicate that the structure of Glu-plasminogen is adapted to oxidation to withstand oxidative stress induced by ROS.

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. Both the radial and oblique views are envisioned to be located in a wide-angle midplane port, which has dimensions that enable simultaneous hosting of the front-end of their quasi-optical (QO) designs. Each QO design will have an in situ hot calibration source in the front-end to provide standalone and calibrated Te (R,t) measurements. The conceptual design for each QO system, the Gaussian beam analysis, and the details of the diagnostic channels are presented.

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. To quantify the improvement in identification accuracy enabled by the current reference library, we ran 1000 Finnish insect and spider species through the Barcode of Life Data system (BOLD) identification engine. Of these, 91% were correctly assigned to a unique species when compared to the new reference library alone, 85% were correctly identified when compared to BOLD with the new material included, and 75% with the new material excluded. To capitalize on this resource, we used the new reference material to train a probabilistic taxonomic assignment tool, FinPROTAX, scoring high success. For the full-length barcode region, the accuracy of taxonomic assignments at the level of classes, orders, families, subfamilies, tribes, genera, and species reached 99.9%, 99.9%, 99.8%, 99.7%, 99.4%, 96.8%, and 88.5%, respectively. The FinBOL arthropod reference library and FinPROTAX are available through the Finnish Biodiversity Information Facility (www.laji.fi) at https://laji.fi/en/theme/protax. Overall, the FinBOL investment represents a massive capacity-transfer from the taxonomic community of Finland to all sectors of society.

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. palustris. Wolf spiders constitute an excellent model for testing the relevance of traditional vs. modern methods in species and population delimitation because several closely related species are distributed over cross-continental geographic ranges. Allopatric populations of the two Pardosa species were sampled across Europe to Far East Russia (latitudinal range > 150°) and several dozen individuals were studied using morphological characters (morphometry of three measures for both sexes, plus five in males only and two in females only), DNA barcoding (COI sequencing) and double-digest restriction site associated DNA sequencing (ddRADseq). The results obtained allow for changing the taxonomic status of two Far East Russian populations to subspecies and ddRADseq proved to be a powerful tool for taxonomic research despite scarce sampling and inherent subjectivity of species delimitation in allopatry. Overall, this study pleads for both multi-criteria and more population-based studies in taxonomy.

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. In the present work, the composition of conjugates of bovine serum albumin and immunoglobulin G with gold nanoparticles obtained by the Turkevich-Frens method are analyzed. The composition was studied by protein fluorescence measurement for particles ranging in size from 20 to 48 nm, depending on the pH of the immobilization medium (from 4 to 5 to 8-10). It was found that a pH shift of the immobilization medium from acidic to alkaline values is accompanied by a change in the mechanism of protein adsorption on the gold surface. In acidic pH conditions (4-5), effective binding of bovine serum albumin and gold nanoparticles occurs throughout the entire range of studied protein concentrations. In alkaline pH conditions (8-10), however, effective binding occurs only at concentrations of >10 µg/mL. This effect is not observed for immunoglobulin G, which is efficiently adsorbed onto nanoparticles throughout the entire range of studied concentrations and pH values. For acidic pH values, the surface of the particles is saturated with the amount of bound proteins, which approximately corresponds to the amount the monolayer is filled. For neutral and alkaline pH values, saturation is not observed and the amount of adsorbed protein certainly exceeds the monolayer filling, leading to multilayer immobilization.