Molecular Characterization of a Novel Enamovirus Infecting Raspberry.

Raspberry plants, valued for their fruits, are vulnerable to a range of viruses that adversely affect their yield and quality. Utilizing high-throughput sequencing (HTS), we identified a novel virus, tentatively named raspberry enamovirus 1 (RaEV1), in three distinct raspberry plants. This study provides a comprehensive characterization of RaEV1, focusing on its genomic structure, phylogeny, and possible transmission routes. Analysis of nearly complete genomes from 14 RaEV1 isolates highlighted regions of variance, particularly marked by indel events. The evidence from phylogenetic and sequence analyses supports the classification of RaEV1 as a distinct species within the Enamovirus genus. Among the 289 plant and 168 invertebrate samples analyzed, RaEV1 was detected in 10.4% and 0.4%, respectively. Most detections occurred in plants that were also infected with other common raspberry viruses. The virus was present in both commercial and wild raspberries, indicating the potential of wild plants to act as viral reservoirs. Experiments involving aphids as potential vectors demonstrated their ability to acquire RaEV1 but not to successfully transmit it to plants.

Mononuclear or Coordination Polymer Complexes? Both Are Possible for 3,6,9-Trioxaundecanedioic Acid.

Investigating the driving forces leading to the formation of a specific supramolecular architecture among a wide spectrum of all the possibly obtainable structures is not an easy task. The contemporary literature provides several models for correctly predicting the thermodynamically accessible structures that can originate from a library of building blocks. Definitions are rigid by their very nature, so their application may sometimes require a shift in perspective. In the study presented herein, we describe the crystal structures of three metallo-supramolecular architectures assembled from deprotonated derivatives of 3,6,9-trioxaundecanedioic acid and Mn(II), Co(II) and Zn(II). In the Mn(II) case, the complexation resulted in a complex of a discrete/heptacoordinated nature, whereas the other two structures appeared as helical polymers. To explain such an anomaly, in this work, we describe how the interplay between the flexibility of the ligand spacer and the number of coordinating atoms involved determines the divergent or convergent organisation of the final coordination architecture.

Heterogeneous Electrochemical Ammonia Oxidation with a Ru-bda Oligomer Anchored on Graphitic Electrodes via CH-π Interactions.

Molecular catalysts can promote ammonia oxidation, providing mechanistic insights into the electrochemical N2 cycle for a carbon-free fuel economy. We report the ammonia oxidation activity of carbon anodes functionalized with the oligomer {[RuII(bda-κ-N 2 O 2)(4,4'-bpy)]10(4,4'-bpy)}, Rubda-10, where bda is [2,2'-bipyridine]-6,6'-dicarboxylate and 4,4'-bpy is 4,4'-bipyridine. Electrocatalytic studies in propylene carbonate demonstrate that the Ru-based hybrid anode used in a 3-electrode configuration transforms NH3 to N2 and H2 in a 1:3 ratio with near-unity faradaic efficiency at an applied potential of 0.1 V vs Fc+/0, reaching turnover numbers of 7500. X-ray absorption spectroscopic analysis after bulk electrolysis confirms the molecular integrity of the catalyst. Based on computational studies together with electrochemical evidence, ammonia nucleophilic attack is proposed as the primary pathway that leads to critical N-N bond formation.

Metamorphic oxygen-evolving molecular Ru and Ir catalysts.

Today sustainable and clean energy conversion strategies are based on sunlight and the use of water as a source of protons and electrons, in a similar manner as it happens in Photosystem II. To achieve this, the charge separation state induced by light has to be capable of oxidising water by 4 protons and 4 electrons and generating molecular oxygen. This oxidation occurs by the intermediacy of a catalyst capable of finding low-energy pathways via proton-coupled electron transfer steps. The high energy involved in the thermodynamics of water oxidation reaction, coupled with its mechanistic complexity, is responsible for the difficulty of discovering efficient and oxidatively robust molecules capable of achieving such a challenging task. A significant number of Ru coordination complexes have been identified as water oxidation catalysts (WOCs) and are among the best understood from a mechanistic perspective. In this review, we describe the catalytic performance of these complexes and focus our attention on the factors that influence their performance during catalysis, especially in cases where a detailed mechanistic investigation has been carried out. The collective information extracted from all the catalysts studied allows one to identify the key features that govern the complex chemistry associated with the catalytic water oxidation reaction. This includes the stability of trans-O-Ru-O groups, the change in coordination number from CN6 to CN7 at Ru high oxidation states, the ligand flexibility, the capacity to undergo intramolecular proton transfer, the bond strain, the axial ligand substitution, and supramolecular effects. Overall, combining all this information generates a coherent view of this complex chemistry.

Mixed Infection of Blackcurrant with a Novel Cytorhabdovirus and Black Currant-Associated Nucleorhabdovirus.

A virome screen was performed on a new breeding line, KB1, of blackcurrant. Rhabdovirus-like particles were observed by electron microscopy in ultrathin sections of flower stalks, and the complete genome sequence of a novel virus, provisionally named blackcurrant rhabdovirus 2 (BCRV2), was determined and verified using high-throughput sequencing. The genomic organization of BCRV2 was characteristic of cytorhabdoviruses (family Rhabdoviridae) and included seven genes: 3 ́- N-P´-P-P3-M-G-L -5 ́. BLASTP analysis revealed that the putative L protein had the highest amino acid sequence identity (75 %) with strawberry virus 2. BCRV2 was detected in Cryptomyzusgaleopsidis, but efficient transmission by this aphid was not confirmed. Of note, we observed coinfection of the KB1 line with blackcurrant-associated rhabdovirus (BCaRV) by RT-PCR. This is likely the first evidence of the presence of a cyto- and a nucleorhabdovirus in a single host.

Online teaching of practical classes under the Covid-19 restrictions.

COVID -19 pandemic and its restrictions bring new challenges to all aspects and phases of higher education. At universities, new remote formats have been developed and deployed for lectures and laboratory exercises. This article addresses challenges and introduces the new experience with lectures and laboratory classes during the pandemic time at the Department of Measurement of the Czech Technical University in Prague, Faculty of Electrical Engineering. Based on the student survey of more than 250 students describes the possibilities of how to adapt the lectures during the lockdown. The article also introduces the Home Lab, a tool developed in the department that helps in distance teaching practical electronic classes. Home Lab includes two parts with functional groups, a Laboratory Experimental Device and a System of Measurement Instruments. The article also shows the opportunity for suitable remote exercises and variants of circuits that can be easily assembled and measured using Software Defined Instrument based on various microcontrollers. A detailed description of all Software Defined Instruments is also present. During the Pandemic, the home lab model was successfully practically verified during distance learning in three subjects, with more than 150 students per semester. It has also been shown that the Home Lab can be successfully deployed for a semester project. The article also presents experience with the teaching software-oriented courses. At the end of the article, practical knowledge and an experience from distance teaching during a three-semester lockdown are shared.

Evaluation of digital watermarking on subjective speech quality.

New methods of securing the distribution of audio content have been widely deployed in the last twenty years. Their impact on perceptive quality has, however, only been seldomly the subject of recent extensive research. We review digital speech watermarking state of the art and provide subjective testing of watermarked speech samples. Latest speech watermarking techniques are listed, with their specifics and potential for further development. Their current and possible applications are evaluated. Open-source software designed to embed watermarking patterns in audio files is used to produce a set of samples that satisfies the requirements of modern speech-quality subjective assessments. The patchwork algorithm that is coded in the application is mainly considered in this analysis. Different watermark robustness levels are used, which allow determining the threshold of detection to human listeners. The subjective listening tests are conducted following ITU-T P.800 Recommendation, which precisely defines the conditions and requirements for subjective testing. Further analysis tries to determine the effects of noise and various disturbances on watermarked speech's perceived quality. A threshold of intelligibility is estimated to allow further openings on speech compression techniques with watermarking. The impact of language or social background is evaluated through an additional experiment involving two groups of listeners. Results show significant robustness of the watermarking implementation, retaining both a reasonable net subjective audio quality and security attributes, despite mild levels of distortion and noise. Extended experiments with Chinese listeners open the door to formulate a hypothesis on perception variations with geographical and social backgrounds.

Synthesis, Structure, and Ammonia Oxidation Catalytic Activity of Ru-NH3 Complexes Containing Multidentate Polypyridyl Ligands.

Ammonia (electro)oxidation with molecular catalysts is a rapidly developing topic with wide practical applications ahead. We report here the catalytic ammonia oxidation reaction (AOR) activity using [Ru(tda-κ-N3O)(py)2], 2, (tda2- is 2,2':6',2''-terpyridine-6,6''-dicarboxylate; py is pyridine) as a catalyst precursor. Furthermore, we also describe the rich chemistry associated with the reaction of Ru-tda and Ru-tPa (tPa-4 is 2,2':6',2''-terpyridine-6,6''-diphosphonate) complexes with NH3 and N2H4 using [RuII(tda-κ-N3O)(dmso)Cl] (dmso is dimethyl sulfoxide) and [RuII(tPa-κ-N3O)(py)2], 8, as synthetic intermediates, respectively. All the new complexes obtained here were characterized spectroscopically by means of UV-vis and NMR. In addition, a crystal X-ray diffraction analysis was performed for complexes trans-[RuII(tda-κ-N3)(py)2(NH3)], 4, trans-[RuII(tda-κ-N3)(N-NH2)(py)2], 5, cis-[RuII(tda-κ-N3)(py)(NH3)2], 6 (30%), and cis-[RuII(tda-k-N3)(dmso)(NH3)2], 7 (70%). The AOR activity associated with 2 and 8 as catalyst precursors was studied in organic and aqueous media. For 2, turnover numbers of 7.5 were achieved under bulk electrolysis conditions at an Eapp = 1.4 V versus normal hydrogen electrode in acetonitrile. A catalytic cycle is proposed based on electrochemical and kinetic evidence.

PFP Compressed Suffix Trees.

Prefix-free parsing (PFP) was introduced by Boucher et al. (2019) as a preprocessing step to ease the computation of Burrows-Wheeler Transforms (BWTs) of genomic databases. Given a string S, it produces a dictionary D and a parse P of overlapping phrases such that BWT(S) can be computed from D and P in time and workspace bounded in terms of their combined size |PFP(S)|. In practice D and P are significantly smaller than S and computing BWT(S) from them is more efficient than computing it from S directly, at least when S is the concatenation of many genomes. In this paper, we consider PFP(S) as a data structure and show how it can be augmented to support full suffix tree functionality, still built and fitting within O(|PFP(S)|) space. This entails the efficient computation of various primitives to simulate the suffix tree: computing a longest common extension (LCE) of two positions in S; reading any cell of its suffix array (SA), of its inverse (ISA), of its BWT, and of its longest common prefix array (LCP); and computing minima over ranges and next/previous smaller value queries over the LCP. Our experimental results show that the PFP suffix tree can be efficiently constructed for very large repetitive datasets and that its operations perform competitively with other compressed suffix trees that can only handle much smaller datasets.

Online teaching at CTU in Prague aka university under COVID restrictions.

Covid-19 related restrictions bring new challenges to all aspects and phases of higher education. At universities, new remote formats are deployed or even developed both for lectures and laboratory exercises. This article addresses new challenges and describes the experience with lessons during the pandemic time at the Department of Measurement of the Czech Technical University in Prague, Faculty of Electrical Engineering. It introduces the best practices exercised using the Home Lab, which helps in distance teaching of practical electronic classes. Home Lab includes two models with functional groups, a Laboratory Experimental Device and System of Measurement Instruments. The article also shows the possibilities of suitable remote exercises and variants of circuits that can be easily assembled and measured using Software Defined Instrument based on STM microcontrollers. During the pandemic, the home lab model was successfully practically verified during distance learning in three classes, with more than 150 students. The article also presents experience with the teaching of software-oriented courses. At first glance, their transformation can be viewed as straightforward. However, practical realization reveals few remarkable details.

Dynamic Helicates Self-Assembly from Homo- and Heterotopic Dynamic Covalent Ligand Strands.

The understanding and the application of reversible covalent reactions and coordination chemistry together with the proper design of the molecular frameworks, allow to achieve not only well-defined output architectures but also different grades of complex behavior. In this work, the dynamic nature of the helical systems offers an additional level of complexity by combining self-sorting on two levels: 1) the build-up of the ligand strand constituents from their components through dynamic covalent chemistry; 2) the assembly of the helicates from the ligands and the metal cations through dynamic metallo-supramolecular chemistry. The information encoded in the ligands constituent molecule was read differently (and accurately at the same time) by metal cations that varied in the coordination algorithms. It enabled the selective formation of a specific type of helicates from a wide library of helicates formed by the possible combination of subcomponents. Ligands containing dynamic tridentate and/or bidentate binding motifs in the same strand were studied to explore the helicates self-assembly with appropriate metal cations.

A Ru-bda Complex with a Dangling Carboxylate Group: Synthesis and Electrochemical Properties.

Ruthenium complexes containing the tetradentate 2,2'-bipyridine-6,6'-dicarboxylato (bda2-) equatorial ligand and ortho-subsituted pyridines in the axial position have been prepared and characterized using spectroscopic, crystallographic and electrochemical techniques. Complexes [Ru(Hbda)(DMSO)(pyC)] (1) and [Ru(bda)(DMSO)(pyA)] (2) (where pyC is 2-pyridinecarboxylate, pyA is pyridine-2-ylmethanol and DMSO is dimethyl sulfoxide) have been isolated in moderate to high yields. The solid state structures of (1-H)- and 2 reveal the strong chelate effect of the axial pyridine ligand that coordinates in a bidentate fashion leaving the bda2- equatorial ligand coordinating in a tridentate mode. In solution, compound 2 shows a dynamic equilibrium between different coordination modes of the bda2- and pyA ligands. This phenomenon does not occur for 1 because the carboxylate binds stronger than the labile alcohol in 2. Cyclic voltammetry analysis of 1 reveals a complex behavior with a pH-independent wave at E1/2 = 1.12 V that is tentatively associated with the two-electron RuIV/II couple. In sharp contrast, complex 2 shows a pH-dependent one-electron wave at E1/2 = 0.83 V (pH 1), assigned to the proton-coupled electron transfer process of the RuIII/II couple and a pH-independent wave at E1/2 = 1.06 V assigned to the RuIV/III couple. Compound 2 is used to prepare complex [Ru(bda)(pic)(pyA)] (4). This complex is air sensitive and converts to complex [Ru(bda)(pic)(pyE)] (5) (where pyE is methyl 2-pyridine carboxylate) in the presence of methanol. This oxidation also occurs by applying a positive potential to an aqueous solution of 4, producing the derivative [Ru(bda)(pic)(pyC)] (3). Cyclic voltammetry of 3 shows two pH-independent one-electron oxidation waves at E1/2 = 0.64 V and E1/2 = 1.0 V, corresponding to the RuIII/II and RuIV/III couples, respectively. In addition, a water oxidation catalytic wave appears at Eonset ≈ 1.4 V. Foot-of-the-wave analysis of this catalytic wave based on a water nucleophilic attack accounts for a TOFmax = 0.63-0.74 s-1.

Subjective speech quality measurement with and without parallel task: Laboratory test results comparison.

This paper focuses on a novel methodology of subjective speech quality measurement and repeatability of its results between laboratory conditions and simulated environmental conditions. A single set of speech samples was distorted by various background noises and low bit-rate coding techniques. This study aimed to compare results of subjective speech quality tests with and without a parallel task deploying the ITU-T P.835 methodology. Afterward, tests results performed with and without a parallel task were compared using Pearson correlation, CI95, and numbers of opposite pair-wise comparisons. The tests show differences in results in the case of a parallel task.

SOPanG: online text searching over a pan-genome.

Motivation: The many thousands of high-quality genomes available now-a-days imply a shift from single genome to pan-genomic analyses. A basic algorithmic building brick for such a scenario is online search over a collection of similar texts, a problem with surprisingly few solutions presented so far. Results: We present SOPanG, a simple tool for exact pattern matching over an elastic-degenerate string, a recently proposed simplified model for the pan-genome. Thanks to bit-parallelism, it achieves pattern matching speeds above 400 MB/s, more than an order of magnitude higher than of other software. Availability and implementation: SOPanG is available for free from: https://github.com/MrAlexSee/sopang. Supplementary information: Supplementary data are available at Bioinformatics online.

Assessment of ECG and respiration recordings from simulated emergency landings of ultra light aircraft.

Pilots of ultra light aircraft have limited training resources, but with the use of low cost simulators it might be possible to train and test some parts of their training on the ground. The purpose of this paper is to examine possibility of stress inducement on a low cost flight simulator. Stress is assessed from electrocardiogram and respiration. Engine failure during flight served as a stress inducement stimuli. For one flight, pilots had access to an emergency navigation system. There were recorded some statistically significant changes in parameters regarding breathing frequency. Although no significant change was observed in ECG parameters, there appears to be an effect on respiration parameters. Physiological signals processed with analysis of variance suggest, that the moment of engine failure and approach for landing affected average breathing frequency. Presence of navigation interface does not appear to have a significant effect on pilots.

Deciphering the growth pattern and phytohormonal content in Saskatoon berry (Amelanchier alnifolia) in response to in vitro cytokinin application.

Clonal propagation plays a critical integral role in the growth and success of a global multi-billion dollar horticulture industry through a constant supply of healthy stock plants. The supply chain depends on continuously improving the micropropagation process, thus, understanding the physiology of in vitro plants remains a core component. We evaluated the influence of exogenously applied cytokinins (CKs, N6-benzyladenine = BA, isopentenyladenine = iP, meta-topolin = mT, 6-(3-hydroxybenzylamino)-9-(tetrahydropyran-2-yl)purine = mTTHP) in Murashige and Skoog (MS)-supplemented media on organogenic response and accumulation of endogenous CK and indole-3-acetic acid (IAA) metabolites. The highest shoot proliferation (30 shoots/explant) was obtained with 20 µM mT treatment. However, the best quality regenerants were produced in 10 µM mT treatment. Rooting of Amelanchier alnifolia in vitro plantlets was observed at the lowest CK concentrations, with the highest root proliferation (3 roots/explant) in 1 µM mTTHP regenerants. Similar to the organogenic response, high levels of endogenous bioactive CK metabolites (free bases, ribosides, and nucleotides) were detected in mT and mTTHP-derived regenerants. The level of O-glucosides was also comparatively high in these cultures. All CK-treated plants had high levels of endogenous free IAA compared to the control. This may suggest an influence of CKs on biosynthesis of IAA.

Coevolution and ratiometric behaviour in metal cation-driven dynamic covalent systems.

Dynamic Covalent Libraries (DCLs) have been used to demonstrate coevolution behaviour on a molecular level using dynamic covalent molecules such as imines and hydrazones. Two systems are presented: the first system is based on a dialdehyde and two diamines in combination with Zn(ii) and Hg(ii) to form a 2 × 2 Constitutional Dynamic Network (CDN) of four complexes of macrocyclic bis-imines. Whereas the two metal ions, when reacted separately form a complex with each macrocycle with low selectivity, when applied together, each cation yields selectively a complex with one of the two macrocycles. Thus, the simultaneous application of both cations, where one might have expected the formation of four different complexes, results in the synergistic evolution (co-evolution) towards a simpler, more selective outcome under agonist amplification. The second system of 4 components, 2 amines and 2 aldehydes displays metalloselection together with a correlated evolution in distribution on complexation of Zn(ii) and Cu(i) with the dynamic ligand constituents and exhibits a dynamic ratiometry process related to the antagonistic behaviour of a pair of ligand constituents.

Training a Constitutional Dynamic Network for Effector Recognition: Storage, Recall, and Erasing of Information.

Constitutional dynamic libraries (CDLs) of hydrazones, acylhydrazones, and imines undergo reorganization and adaptation in response to chemical effectors (herein metal cations) via component exchange and selection. Such CDLs can be subjected to training by exposition to given effectors and keep memory of the information stored by interaction with a specific metal ion. The long-term storage of the acquired information into the set of constituents of the system allows for fast recognition on subsequent contacts with the same effector(s). Dynamic networks of constituents were designed to adapt orthogonally to different metal cations by up- and down-regulation of specific constituents in the final distribution. The memory may be erased by component exchange between the constituents so as to regenerate the initial (statistical) distribution. The libraries described represent constitutional dynamic systems capable of acting as information storage molecular devices, in which the presence of components linked by reversible covalent bonds in slow exchange and bearing adequate coordination sites allows for the adaptation to different metal ions by constitutional variation. The system thus performs information storage, recall, and erase processes.

Gallium(III) complexes of NOTA-bis (phosphonate) conjugates as PET radiotracers for bone imaging.

Ligands with geminal bis(phosphonic acid) appended to 1,4,7-triazacyclonone-1,4-diacetic acid fragment through acetamide (NOTAM(BP) ) or methylenephosphinate (NO2AP(BP) ) spacers designed for (68) Ga were prepared. Ga(III) complexation is much faster for ligand with methylenephosphinate spacer than that with acetamide one, in both chemical (high reactant concentrations) and radiolabeling studies with no-carrier-added (68) Ga. For both ligands, formation of Ga(III) complex was slower than that with NOTA owing to the strong out-of-cage binding of bis(phosphonate) group. Radiolabeling was efficient and fast only above 60 °C and in a narrow acidity region (pH ~3). At higher temperature, hydrolysis of amide bond of the carboxamide-bis(phosphonate) conjugate was observed during complexation reaction leading to Ga-NOTA complex. In vitro sorption studies confirmed effective binding of the (68) Ga complexes to hydroxyapatite being comparable with that found for common bis(phosphonate) drugs such as pamindronate. Selective bone uptake was confirmed in healthy rats by biodistribution studies ex vivo and by positron emission tomography imaging in vivo. Bone uptake was very high, with SUV (standardized uptake value) of 6.19 ± 1.27 for [(68) Ga]NO2AP(BP) ) at 60 min p.i., which is superior to uptake of (68) Ga-DOTA-based bis(phosphonates) and [(18) F]NaF reported earlier (SUV of 4.63 ± 0.38 and SUV of 4.87 ± 0.32 for [(68) Ga]DO3AP(BP) and [(18) F]NaF, respectively, at 60 min p.i.). Coincidently, accumulation in soft tissue is generally low (e.g. for kidneys SUV of 0.26 ± 0.09 for [(68) Ga]NO2AP(BP) at 60 min p.i.), revealing the new (68) Ga complexes as ideal tracers for noninvasive, fast and quantitative imaging of calcified tissue and for metastatic lesions using PET or PET/CT.

Calix[4]arenes with intramolecularly bridged meta positions prepared via Pd-catalysed double C-H activation.

The introduction of a 2-pyridylsulfoxide moiety into the upper rim of calix[4]arenes enabled the synthesis of unprecedented derivatives with intramolecularly bridged meta positions of two neighbouring aromatic subunits. Palladium-catalysed double C-H activation thus represents a straightforward way to a completely novel type of calixarenes.