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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.
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Hipersensibilidade , Vírus , Animais , Transdução de Sinais , Antivirais , Proteínas NLR , FagocitoseRESUMO
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.
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Afídeos , Potyvirus , Solanum tuberosum , Animais , Potyvirus/genética , Doenças das Plantas , Solanum tuberosum/genética , Federação Russa , Genoma Viral , Afídeos/genéticaRESUMO
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.
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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.
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Evolução Molecular , Variação Genética , Vírus Eruptivo da Ameixa/classificação , Vírus Eruptivo da Ameixa/isolamento & purificação , Prunus domestica/virologia , Recombinação Genética , Análise por Conglomerados , Genoma Viral , Filogenia , Vírus Eruptivo da Ameixa/genética , Federação Russa , Análise de Sequência de DNARESUMO
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.
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Variação Genética , Genoma Viral/genética , Doenças das Plantas/virologia , Vírus Eruptivo da Ameixa/genética , Prunus avium/virologia , Filogenia , Vírus Eruptivo da Ameixa/isolamento & purificação , Federação Russa , Análise de Sequência de DNARESUMO
Numerous plum pox virus (PPV) strain D isolates have been found in geographically distant regions of European Russia and the Crimean peninsula on different stone fruit hosts. Phylogenetic analysis of their partial and complete genomes suggests multiple introductions of PPV-D into Russia. Distinct natural isolates from Prunus tomentosa were found to bear unique amino acid substitutions in the N-terminus of the coat protein (CP) that may contribute to the adaptation of PPV-D to this host. Serological analysis using the PPV-D-specific monoclonal antibody 4DG5 provided further evidence that mutations at positions 58 and 59 of the CP are crucial for antibody binding.
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Variação Genética , Doenças das Plantas/virologia , Vírus Eruptivo da Ameixa/isolamento & purificação , Anticorpos Monoclonais/imunologia , Anticorpos Antivirais/imunologia , Proteínas do Capsídeo/genética , Proteínas do Capsídeo/imunologia , Análise por Conglomerados , Genoma Viral , Dados de Sequência Molecular , Filogenia , Vírus Eruptivo da Ameixa/classificação , Vírus Eruptivo da Ameixa/genética , Vírus Eruptivo da Ameixa/imunologia , Ligação Proteica , RNA Viral/genética , Federação Russa , Análise de Sequência de DNA , Homologia de SequênciaRESUMO
Atypical isolates of plum pox virus (PPV) were discovered in naturally infected sour cherry in urban ornamental plantings in Moscow, Russia. The isolates were detected by polyclonal double antibody sandwich ELISA and RT-PCR using universal primers specific for the 3'-non-coding and coat protein (CP) regions of the genome but failed to be recognized by triple antibody sandwich ELISA with the universal monoclonal antibody 5B and by RT-PCR using primers specific to for PPV strains D, M, C and W. Sequence analysis of the CP genes of nine isolates revealed 99.2-100 % within-group identity and 62-85 % identity to conventional PPV strains. Phylogenetic analysis showed that the atypical isolates represent a group that is distinct from the known PPV strains. Alignment of the N-terminal amino acid sequences of CP demonstrated their close similarity to those of a new tentative PPV strain, CR.
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Doenças das Plantas/virologia , Vírus Eruptivo da Ameixa/isolamento & purificação , Prunus/virologia , Sequência de Bases , Ensaio de Imunoadsorção Enzimática , Dados de Sequência Molecular , Filogenia , Vírus Eruptivo da Ameixa/genética , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Alinhamento de SequênciaRESUMO
The Jahn-Teller effect explains distortions and nondegenerate energy levels in molecular and solid-state physics via a coupling of effective spins to collective bosons. Here we propose and theoretically analyze the quantum simulation of a many-body Jahn-Teller model with linear ion crystals subjected to magnetic field gradients. We show that the system undergoes a quantum magnetic structural phase transition which leads to a reordering of particle positions and the formation of a spin-phonon quasicondensate in mesoscopic ion chains.
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In studying the distribution and genetic diversity of Plum pox virus (PPV) in Russia, over a dozen new PPV isolates belonging to the strain Winona (PPV-W) were identified by immunocapture reverse-transcription polymerase chain reaction with the PPV-W-specific primers 3174-SP-F3/3174-SP-R1. Isolates were detected in two geographically distant regions of European Russia (Northern Caucasus and Moscow regions) in naturally infected plum (Prunus domestica), blackthorn (P. spinosa), Canadian plum (P. nigra), and downy cherry (P. tomentosa). The new PPV-W isolates were shown to be serologically related but not identical by triple-antibody sandwich enzyme-linked immunosorbent assay and Western blotting analysis using the monoclonal antibody (MAb) 5B-IVIA and MAbs specific to the N-terminal epitopes of PPV-W isolate 3174. Analysis of nucleotide and deduced amino acid sequences of the (C-ter)NIb-(N-ter)CP genome region indicate great genetic diversity among isolates, with phylogenetic analysis revealing seven clades. Isolates P1 and P3 found in plum in the south of Russia clustered closely with the putative ancestral PPV-W isolate LV-145bt from Latvia, while isolate 1410-7 found in P. nigra in Moscow appears to be closely related to the Canadian isolate W3174. The data obtained indicate wide dissemination of PPV-W isolate in stone fruit in the European part of the former USSR.
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The effect of humic acid (HA) on U(VI) sorption on bentonite was studied in batch experiments at room temperature and ambient atmosphere at a (237)U(VI) concentration of 8.4 × 10(-11) M and HA concentration of 100 mg L(-1). The distribution of U(VI) between the liquid and solid phases was studied as a function of pH and ionic strength both in the absence and presence of HA. It was shown that the uranyl sorption on bentonite is strongly dependent on pH and the presence of humics, and the effect of the addition order was negligible. In the absence of HA an enhancement in the uptake with increasing pH was observed and a sharp sorption edge was found to take place between pH 3.2 and 4.2. The presence of HA slightly increases uranium(VI) sorption at low pH and curtails it at moderate pH, compared to the absence of HA. In the basic pH range for both the presence and absence of HA the sorption of uranium is significantly reduced, which could be attributed to the formation of soluble uranyl carbonate complexes. The influence of ionic strength on U(VI) and HA uptake by bentonite were investigated in the range of 0.01-1.0 M, and while there was an enhancement in the sorption of humic acid with increasing ionic strength, no significant effect of the ionic strength on the U(VI) sorption was observed in both the absence and presence of HA.
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Bentonita/química , Poluentes do Solo/química , Solo/química , Urânio/química , Adsorção , Substâncias Húmicas , Concentração de Íons de Hidrogênio , Concentração Osmolar , Poluentes do Solo/análise , Urânio/análiseRESUMO
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.
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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.
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A southeastern European isolate of Alternanthera mosaic virus (AltMV-MU) of the genus Potexvirus (family Flexiviridae) was purified from the ornamental plant Portulaca grandiflora. The complete nucleotide sequence (6606 nucleotides) of AltMV-MU genomic RNA was defined. The AltMV-MU genome is different from those of all isolates described earlier and is most closely related to genomes of partly sequenced portulaca isolates AltMV-Po (America) and AltMV-It (Italy). Phylogenetic analysis supports the view that AltMV-MU belongs to a new "portulaca" genotype distinguishable from the "phlox" genotype.
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Genoma Viral , Folhas de Planta/virologia , Portulaca/virologia , Potexvirus/classificação , Sequência de Aminoácidos , Sequência de Bases , Proteínas do Capsídeo/genética , Dados de Sequência Molecular , Filogenia , Doenças das Plantas/genética , Doenças das Plantas/virologia , Potexvirus/genética , Potexvirus/isolamento & purificação , RNA Viral , RNA Polimerase Dependente de RNA/genéticaRESUMO
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.
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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.
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Vacinas contra Antraz , Antraz , Bacillus anthracis , Toxinas Bacterianas , Antraz/prevenção & controle , Vacinas contra Antraz/genética , Anticorpos Antibacterianos , Antígenos de Bactérias/genética , Bacillus anthracis/genética , Toxinas Bacterianas/genética , Humanos , Proteínas Recombinantes/genéticaRESUMO
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.
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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.
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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.
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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.
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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.