The Temporal and Geographical Dynamics of Potato Virus Y Diversity in Russia.

Potato virus Y, an important viral pathogen of potato, has several genetic variants and geographic distributions which could be affected by environmental factors, aphid vectors, and reservoir plants. PVY is transmitted to virus-free potato plants by aphids and passed on to the next vegetative generations through tubers, but the effects of tuber transmission in PVY is largely unknown. By using high-throughput sequencing, we investigated PVY populations transmitted to potato plants by aphids in different climate zones of Russia, namely the Moscow and Astrakhan regions. We analyzed sprouts from the tubers produced by field-infected plants to investigate the impact of tuber transmission on PVY genetics. We found a significantly higher diversity of PVY isolates in the Astrakhan region, where winters are shorter and milder and summers are warmer compared to the Moscow region. While five PVY types, NTNa, NTNb, N:O, N-Wi, and SYR-I, were present in both regions, SYRI-II, SYRI-III, and 261-4 were only found in the Astrakhan region. All these recombinants were composed of the genome sections derived from PVY types O and N, but no full-length sequences of such types were present. The composition of the PVY variants in the tuber sprouts was not always the same as in their parental plants, suggesting that tuber transmission impacts PVY genetics.

Signaling and Resistosome Formation in Plant Innate Immunity to Viruses: Is There a Common Mechanism of Antiviral Resistance Conserved across Kingdoms?

Virus-specific proteins, including coat proteins, movement proteins, replication proteins, and suppressors of RNA interference are capable of triggering the hypersensitive response (HR), which is a type of cell death in plants. The main cell death signaling pathway involves direct interaction of HR-inducing proteins with nucleotide-binding leucine-rich repeats (NLR) proteins encoded by plant resistance genes. Singleton NLR proteins act as both sensor and helper. In other cases, NLR proteins form an activation network leading to their oligomerization and formation of membrane-associated resistosomes, similar to metazoan inflammasomes and apoptosomes. In resistosomes, coiled-coil domains of NLR proteins form Ca2+ channels, while toll-like/interleukin-1 receptor-type (TIR) domains form oligomers that display NAD+ glycohydrolase (NADase) activity. This review is intended to highlight the current knowledge on plant innate antiviral defense signaling pathways in an attempt to define common features of antiviral resistance across the kingdoms of life.

Designing Stable Bacillus anthracis Antigens with a View to Recombinant Anthrax Vaccine Development.

Anthrax is a disease caused by Bacillus anthracis that affects mammals, including humans. Recombinant B. anthracis protective antigen (rPA) is the most common basis for modern anthrax vaccine candidates. However, this protein is characterised by low stability due to proteolysis and deamidation. Here, for the first time, two modification variants leading to full-size rPA stabilisation have been implemented simultaneously, through deamidation-prone asparagine residues substitution and by inactivation of proteolysis sites. Obtained modified rPA (rPA83m) has been demonstrated to be stable in various temperature conditions. Additionally, rPA1+2 containing PA domains I and II and rPA3+4 containing domains III and IV, including the same modifications, have been shown to be stable as well. These antigens can serve as the basis for a vaccine, since the protective properties of PA can be attributed to individual PA domains. The stability of each of three modified anthrax antigens has been considerably improved in compositions with tobacco mosaic virus-based spherical particles (SPs). rPA1+2/rPA3+4/rPA83m in compositions with SPs have maintained their antigenic specificity even after 40 days of incubation at +37 °C. Considering previously proven adjuvant properties and safety of SPs, their compositions with rPA83m/rPA1+2/rPA3+4 in any combinations might be suitable as a basis for new-generation anthrax vaccines.

Vaccine Candidate Against COVID-19 Based on Structurally Modified Plant Virus as an Adjuvant.

A recombinant vaccine candidate has been developed based on the major coronaviruses' antigen (S protein) fragments and a novel adjuvant-spherical particles (SPs) formed during tobacco mosaic virus thermal remodeling. The receptor-binding domain and the highly conserved antigenic fragments of the S2 protein subunit were chosen for the design of recombinant coronavirus antigens. The set of three antigens (Co1, CoF, and PE) was developed and used to create a vaccine candidate composed of antigens and SPs (SPs + 3AG). Recognition of SPs + 3AG compositions by commercially available antibodies against spike proteins of SARS-CoV and SARS-CoV-2 was confirmed. The immunogenicity testing of these compositions in a mouse model showed that SPs improved immune response to the CoF and PE antigens. Total IgG titers against both proteins were 9-16 times higher than those to SPs. Neutralizing activity against SARS-CoV-2 in serum samples collected from hamsters immunized with the SPs + 3AG was demonstrated.

Plum Pox Virus Strain C Isolates Can Reduce Sour Cherry Productivity.

The impact of plum pox virus (PPV) on sour cherry (Prunus cerasus L.) productivity has been studied by comparing the yield of PPV-infected and PPV-free fruit-bearing trees. A total of 152 16- to 17-year-old trees of nine cultivars and hybrids were surveyed in the production orchards (cultivar collection and hybrid testing plots) in the Republic of Tatarstan, Russia. Sixty trees tested positive for PPV using ELISA and RT-PCR. Among them, 58 PPV isolates belonged to the strain C and the other 2 isolates to the strain CV. For the cultivars Sevastyanovskaya, Shakirovskaya, hybrids 88-2 and 80-8, the average (2012 to 2019) productivity of infected trees was 38% to 45% lower than for PPV-free trees of the same cultivar or hybrid. No ilarviruses (prunus necrotic ringspot virus, prune dwarf virus, apple mosaic virus, American plum line pattern virus) were detected in PPV-infected trees, suggesting that reduced cherry productivity was attributed to the PPV infection. Thus, it was shown for the first time that PPV can reduce the productivity of at least some sour cherry cultivars and hybrids, and strain C isolates are responsible for crop losses.

Enhanced Parameter Estimation with Periodically Driven Quantum Probe.

I propose a quantum metrology protocol for measuring frequencies and weak forces based on a periodic modulating quantum Jahn-Teller system composed of a single spin and two bosonic modes. I show that, in the first order of the frequency drive, the time-independent effective Hamiltonian describes spin-dependent interaction between the two bosonic modes. In the limit of high-frequency drive and low bosonic frequency, the quantum Jahn-Teller system exhibits critical behavior which can be used for high-precision quantum estimation. A major advantage of the scheme is the robustness of the system against spin decoherence, which allows it to perform parameter estimation with measurement time not limited by spin dephasing.

CERN-MEDICIS: A Review Since Commissioning in 2017.

The CERN-MEDICIS (MEDical Isotopes Collected from ISolde) facility has delivered its first radioactive ion beam at CERN (Switzerland) in December 2017 to support the research and development in nuclear medicine using non-conventional radionuclides. Since then, fourteen institutes, including CERN, have joined the collaboration to drive the scientific program of this unique installation and evaluate the needs of the community to improve the research in imaging, diagnostics, radiation therapy and personalized medicine. The facility has been built as an extension of the ISOLDE (Isotope Separator On Line DEvice) facility at CERN. Handling of open radioisotope sources is made possible thanks to its Radiological Controlled Area and laboratory. Targets are being irradiated by the 1.4 GeV proton beam delivered by the CERN Proton Synchrotron Booster (PSB) on a station placed between the High Resolution Separator (HRS) ISOLDE target station and its beam dump. Irradiated target materials are also received from external institutes to undergo mass separation at CERN-MEDICIS. All targets are handled via a remote handling system and exploited on a dedicated isotope separator beamline. To allow for the release and collection of a specific radionuclide of medical interest, each target is heated to temperatures of up to 2,300°C. The created ions are extracted and accelerated to an energy up to 60 kV, and the beam steered through an off-line sector field magnet mass separator. This is followed by the extraction of the radionuclide of interest through mass separation and its subsequent implantation into a collection foil. In addition, the MELISSA (MEDICIS Laser Ion Source Setup At CERN) laser laboratory, in service since April 2019, helps to increase the separation efficiency and the selectivity. After collection, the implanted radionuclides are dispatched to the biomedical research centers, participating in the CERN-MEDICIS collaboration, for Research & Development in imaging or treatment. Since its commissioning, the CERN-MEDICIS facility has provided its partner institutes with non-conventional medical radionuclides such as Tb-149, Tb-152, Tb-155, Sm-153, Tm-165, Tm-167, Er-169, Yb-175, and Ac-225 with a high specific activity. This article provides a review of the achievements and milestones of CERN-MEDICIS since it has produced its first radioactive isotope in December 2017, with a special focus on its most recent operation in 2020.

Novel antigen panel for modern broad-spectrum recombinant rotavirus A vaccine.

PURPOSE: Recombinant rotavirus A vaccines are being developed as an alternative to existing live oral attenuated vaccines. One of the main problems in the production of such vaccines is the genetic diversity of the strains that are in circulation. The goal of this study was to create an antigen panel for modern broad-spectrum recombinant rotavirus A vaccine. MATERIALS AND METHODS: The antigens of rotavirus were cloned and expressed in Escherichia coli. Antigenic specificity was investigated by Western blot analysis, which was performed using commercial polyclonal antisera to several RVA strains. Phylogenetic analysis was based on the amino acid sequences of the VP8* protein fragment of human RVA isolates representing genotypes P[4], P[6], and P[8]. RESULTS: A universal panel of antigens was established, including consensus and conserved sequences of structural proteins VP8*, VP5*, and VP7, which are the main targets of neutralizing antibodies. For the first time, a consensus approach was used in the design of extended antigens based on VP8* (genotypes P[4], P[6], and P[8]) and VP5* (genotype P[8]) proteins' fragments. In addition, a gene coding the protein (ep-875) containing several copies of conserved short neutralizing epitopes of VP8*, VP7, and VP5* was created. Western blot analysis demonstrated that three synthetic VP8*-based antigens were not recognized by commercial antiserum against rotavirus strains isolated more than 35 years ago, but the specific activity of the VP5* and ep-875 antigens was confirmed. The problems of serological mismatch of vaccine strains and antigens with currently circulating strains are discussed. CONCLUSION: Five antigens representing sequences of structural proteins belonging to different genotypes can be used in various combinations (from mono- to pentavalent mixtures) for the development of an effective broad-spectrum rotavirus vaccine.

Ra-224 activity, half-life, and 241 keV gamma ray absolute emission intensity: A NIST-NPL bilateral comparison.

The national metrology institutes for the United Kingdom (UK) and the United States of America (USA) have compared activity standards for 224Ra, an α-particle emitter of interest as the basis for therapeutic radiopharmaceuticals. Solutions of 224RaCl2 were assayed by absolute methods, including digital coincidence counting and triple-to-double coincidence ratio liquid scintillation counting. Ionization chamber and high-purity germanium (HPGe) γ-ray spectrometry calibrations were compared; further, a solution was shipped between laboratories for a direct comparison by HPGe spectrometry. New determinations of the absolute emission intensity for the 241 keV γ ray (Iγ = 4.011(16) per 100 disintegrations of 224Ra) and of the 224Ra half-life (T1/2 = 3.6313(14) d) are presented and discussed in the context of previous measurements and evaluations.

Two approaches for the stabilization of Bacillus anthracis recombinant protective antigen.

Anthrax is a zoonotic disease caused by the gram-positive spore-forming bacteria Bacillus anthracis. There is a need for safe, highly effective, long-term storage vaccine formulations for mass vaccination. However, the development of new subunit vaccines based on recombinant protective antigen (rPA) faces the problem of vaccine antigen instability. Here, the potential of simultaneous application of two different approaches to stabilize rPA was demonstrated. Firstly, we employed spherical particles (SPs) obtained from the tobacco mosaic virus (TMV). Previously, we had reported that SPs can serve as an adjuvant and platform for antigen presentation. In the current work, SPs were shown to increase the stability of the full-size rPA without loss of its antigenic properties. The second direction was site-specific mutagenesis of asparagine residues to avoid deamidation that causes partial protein degradation. The modified recombinant protein comprising the PA immunogenic domains 3 and 4 (rPA3 + 4) was stable during storage at 4 and 25°C. rPA3 + 4 interacts with antibodies to rPA83 both individually and as a part of a complex with SPs. The results obtained can underpin the development of a recombinant vaccine with a full-size modified rPA (with similar amino acid substitutions that stabilize the protein) and SPs.

Graphene Flakes for Electronic Applications: DC Plasma Jet-Assisted Synthesis.

The possibility of graphene synthesis (the bottom-up approach) in plasma and the effective control of the morphology and electrical properties of graphene-based layers were demonstrated. Graphene flakes were grown in a plasma jet generated by a direct current plasma torch with helium and argon as the plasma-forming gases. In the case of argon plasma, the synthesized graphene flakes were relatively thick (2-6 nm) and non-conductive. In helium plasma, for the first time, graphene with a predominance of monolayer flakes and high conductivity was grown in a significant amount using an industrial plasma torch. One-dimensional (1D) flow modeling shows that the helium plasma is a less charged environment providing the formation of thinner graphene flakes with low defect density. These flakes might be used for a water-based suspension of the graphene with PEDOT:PSS (poly(3,4-ethylenedioxythiophene): polystyrene sulfonate) composite to create the structures employing the 2D printing technologies. Good structural quality, low layer resistance, and good mechanical strength combined with the ability to obtain a large amount of the graphene powder, and to control the parameters of the synthesized particles make this material promising for various applications and, above all, for sensors and other devices for flexible electronics and the Internet of things ecosystem.

Distinctive Features of Graphene Synthesized in a Plasma Jet Created by a DC Plasma Torch.

Synthesis of graphene materials in a plasma stream from an up to 40 kW direct current (DC) plasma torch is investigated. These materials are created by means of the conversion of hydrocarbons under the pressure 350-710 Torr without using catalysts, without additional processes of inter-substrate transfer and the elimination of impurities. Helium and argon are used as plasma-forming gas, propane, butane, methane, and acetylene are used as carbon precursors. Electron microscopy and Raman imaging show that synthesis products represent an assembly of flakes varying in the thickness and the level of deformity. An occurrence of hydrogen in the graphene flakes is discovered by X-ray photoelectron spectroscopy, thermal analysis, and express-gravimetry. Its quantity depends on the type of carrier gas. Quasi-one-dimensional approach under the local thermodynamic equilibrium was used to investigate the evolution of the composition of helium and argon plasma jets with hydrocarbon addition. Hydrogen atoms appear in the hydrogen-rich argon jet under higher temperature. This shows that solid particles live longer in the hydrogen-rich environment compared with the helium case providing some enlargement of graphene with less hydrogen in its structure. In conclusion, graphene in flakes appears because of the volumetric synthesis in the hydrogen environment. The most promising directions of the practical use of graphеne flakes are apparently related to structural ceramics.

Two-qubit quantum gate and entanglement protected by circulant symmetry.

We propose a method for the realization of the two-qubit quantum Fourier transform (QFT) using a Hamiltonian which possesses the circulant symmetry. Importantly, the eigenvectors of the circulant matrices are the Fourier modes and do not depend on the magnitude of the Hamiltonian elements as long as the circulant symmetry is preserved. The QFT implementation relies on the adiabatic transition from each of the spin product states to the respective quantum Fourier superposition states. We show that in ion traps one can obtain a Hamiltonian with the circulant symmetry by tuning the spin-spin interaction between the trapped ions. We present numerical results which demonstrate that very high fidelity can be obtained with realistic experimental resources. We also describe how the gate can be accelerated by using a "shortcut-to-adiabaticity" field.

Chemical Purification of Terbium-155 from Pseudo-Isobaric Impurities in a Mass Separated Source Produced at CERN.

Four terbium radioisotopes (149, 152, 155, 161Tb) constitute a potential theranostic quartet for cancer treatment but require any derived radiopharmaceutical to be essentially free of impurities. Terbium-155 prepared by proton irradiation and on-line mass separation at the CERN-ISOLDE and CERN-MEDICIS facilities contains radioactive 139Ce16O and also zinc or gold, depending on the catcher foil used. A method using ion-exchange and extraction chromatography resins in two column separation steps has been developed to isolate 155Tb with a chemical yield of ≥95% and radionuclidic purity ≥99.9%. Conversion of terbium into a form suitable for chelation to targeting molecules in diagnostic nuclear medicine is presented. The resulting 155Tb preparations are suitable for the determination of absolute activity, SPECT phantom imaging studies and pre-clinical trials.

Compensation of the trap-induced quadrupole interaction in trapped Rydberg ions.

The quadrupole interaction between the Rydberg electronic states of a Rydberg ion and the radio frequency electric field of the ion trap is analyzed. Such a coupling is negligible for the lowest energy levels of a trapped ion but it is important for a trapped Rydberg ion due to its large electric quadrupole moment. This coupling cannot be neglected by the standard rotating-wave approximation because it is comparable to the frequency of the trapping electric field. We investigate the effect of the quadrupole coupling by performing a suitable effective representation of the Hamiltonian. For a single ion we show that in this effective picture the quadrupole interaction is replaced by rescaled laser intensities and additional Stark shifts of the Rydberg levels. Hence this detrimental quadrupole coupling can be efficiently compensated by an appropriate increase of the Rabi frequencies. Moreover, we consider the strong dipole-dipole interaction between a pair of Rydberg ions in the presence of the quadrupole coupling. In the effective representation we observe reducing of the dipole-dipole coupling as well as additional spin-spin interaction.

Sequence Analysis of Plum pox virus Strain C Isolates from Russia Revealed Prevalence of the D96E Mutation in the Universal Epitope and Interstrain Recombination Events.

The understanding of genetic diversity, geographic distribution, and antigenic properties of Plum pox virus (PPV) is a prerequisite to improve control of sharka, the most detrimental viral disease of stone fruit crops worldwide. Forty new PPV strain C isolates were detected in sour cherry (Prunus cerasus) from three geographically distant (700⁻1100 km) regions of European Russia. Analysis of their 3'-terminal genomic sequences showed that nineteen isolates (47.5%) bear the D96E mutation in the universal epitope of the coat protein. Almost all of them cannot be detected by the monoclonal antibody 5B in triple antibody sandwich enzyme-linked immunosorbent assayand Western blot analysis that may potentially compromise serological PPV detection in cherries. Full-length genomes of seven PPV-C isolates were determined employing next-generation sequencing. Using the Recombination Detection Program (RDP4), the recombination event covering the region from (Cter)P1 to the middle of the HcPro gene was predicted in all the available PPV-C complete genomes. The isolates Tat-4, belonging to the strain CV, and RU-17sc (PPV-CR) were inferred as major and minor parents, respectively, suggesting possible pathways of evolution of the cherry-adapted strains. Downy cherry (P. tomentosa) was identified as the natural PPV-C host for the first time.

Molecular characterization of Plum pox virus Rec isolates from Russia suggests a new insight into evolution of the strain.

Field isolates of Plum pox virus (PPV), belonging to the strain Rec, have been found for the first time in Russia. Full-size genomes of the isolates K28 and Kisl-1pl from myrobalan and plum, respectively, were sequenced on the 454 platform. Analysis of all known PPV-Rec complete genomes using the Recombination Detection Program (RDP4) revealed yet another recombination event in the 5'-terminal region. This event was detected by seven algorithms, implemented in the RDP4, with statistically significant P values and supported by a phylogenetic analysis with the bootstrap value of 87%. A putative PPV-M-derived segment, encompassing the C-terminus of the P1 gene and approximately two-thirds of the HcPro gene, is bordered by breakpoints at positions 760-940 and 1838-1964, depending on the recombinant isolate. The predicted 5'-distal breakpoint for the isolate Valjevka is located at position 2804. The Dideron (strain D) and SK68 (strain M) isolates were inferred as major and minor parents, respectively. Finding of another recombination event suggests more complex evolutionary history of PPV-Rec than previously assumed. Perhaps the first recombination event led to the formation of a PPV-D variant harboring the PPV-M-derived fragment within the 5'-proximal part of the genome. Subsequent recombination of its descendant with PPV-M in the 3'-proximal genomic region resulted in the emergence of the evolutionary successful strain Rec.

Analysis of Genetic Diversity of Russian Sour Cherry Plum pox virus Isolates Provides Evidence of a New Strain.

Plum pox virus (PPV) exists as a complex of nine strains adapted to different Prunus hosts. Unusual PPV isolates that do not belong to the known cherry-adapted strains were discovered on sour cherry in Russia. Here, two complete genomes of isolates Tat-2 and Tat-4 were determined by sequencing on the Illumina HiSeq 2500 platform. Both were composed of 9,792 nucleotides, excluding the poly(A) tail, with the organization typical of PPV and had 99.4 and 99.7% identity between each other at the nucleotide and amino acid levels. The sequence identities between Tat-2/Tat-4 and known PPV strains ranged from 77.6 to 83.3% for genomic RNA and from 80.0 to 93.8% for polyprotein. Phylogenetic analysis placed Tat-2 and Tat-4 in a separate clade, distinct from the C and CR strains. Three more Tat-2/Tat-4-like isolates were detected in local cherry plantings using the newly developed, specific RT-PCR assay. Based on the phylogenetic analysis, sequence identities, and environmental distribution, Tat-2, Tat-4, and related isolates represent a new cherry-adapted PPV strain for which the name PPV-CV (Cherry Volga) is proposed.

Consensus evaluation of radioactivity-in-soil reference materials in the context of an NPL Environmental Radioactivity Proficiency Test Exercise.

The development of two radioactivity-in-soil reference materials is described - one for peat and one for soil with high sand content. Each bulk material was processed, subdivided and measured before being sent to participants in an NPL Environmental Radioactivity Proficiency Test Exercise. Activity concentrations of radionuclides in each material were determined by 'consensus' evaluations of participants' results using two weighted mean methods. The project demonstrated the use of such exercises in delivering reference materials to the user community.

New highly divergent Plum pox virus isolates infecting sour cherry in Russia.

Unusual Plum pox virus (PPV) isolates (named Tat isolates) were discovered on sour cherry (Prunus cerasus) in Russia. They failed to be recognized by RT-PCR using commonly employed primers specific to the strains C or CR (the only ones that proved able to infect sour cherry) as well as to the strains M and W. Some of them can be detected by RT-PCR using the PPV-D-specific primers P1/PD or by TAS-ELISA with the PPV-C-specific monoclonal antibody AC. Phylogenetic analysis of the 3'-terminal genomic region assigned the Tat isolates into the cluster of cherry-adapted strains. However, they grouped separately from the C and CR strains and from each other as well. The sequence divergence of the Tat isolates is comparable to the differences between the known PPV strains. They may represent new group(s) of cherry-adapted isolates which do not seem to belong to any known strain of the virus.