Nucleotide sequence and genomic organization of an ophiovirus associated with lettuce big-vein disease

The complete nucleotide sequence of an ophiovirus associated with lettuce big-vein disease has been elucidated. The genome consisted of four RNA molecules of approximately 7ò8, 1ò7, 1ò5 and 1ò4 kb. Virus particles were shown to contain nearly equimolar amounts of RNA molecules of both polarities. The 5'- and 3'-terminal ends of the RNA molecules are largely, but not perfectly, complementary to each other. The virus genome contains seven open reading frames. Database searches with the putative viral products revealed homologies with the RNA-dependent RNA polymerases of rhabdoviruses and Ranunculus white mottle virus, and the capsid protein of Citrus psorosis virus. The gene encoding the viral polymerase appears to be located on the RNA segment 1, while the nucleocapsid protein is encoded by the RNA3. No significant sequence similarities were observed with other viral proteins. In spite of the morphological resemblance with species in the genus Tenuivirus, the ophioviruses appear not to be evolutionary closely related to this genus nor any other viral genus

Sequence analysis and genomic organization of Aphid lethal paralysis virus: a new member of the family Dicistroviridae

The complete nucleotide sequence of the genomic RNA of an aphid-infecting virus, Aphid lethal paralysis virus (ALPV), has been determined. The genome is 9812 nt in length and contains two long open reading frames (ORFs), which are separated by an intergenic region of 163 nt. The first ORF (5' ORF) is preceded by an untranslated leader sequence of 506 nt, while an untranslated region of 571 nt follows the second ORF (3' ORF). The deduced amino acid sequences of the 5' ORF and 3' ORF products respectively showed similarity to the non-structural and structural proteins of members of the newly recognized genus Cripavirus (family Dicistroviridae). On the basis of the observed sequence similarities and identical genome organization, it is proposed that ALPV belongs to this genus. Phylogenetic analysis showed that ALPV is most closely related to Rhopalosiphum padi virus, and groups in a cluster with Drosophila C virus and Cricket paralysis virus, while the other members of this genus are more distantly related. Infectivity experiments showed that ALPV can not only infect aphid species but is also able to infect the whitefly Trialeurodes vaporariorum, extending its host range to another family of the order Hemipter

Learning Layer-wise Equivariances Automatically using Gradients

Convolutions encode equivariance symmetries into neural networks leading to better generalisation performance. However, symmetries provide fixed hard constraints on the functions a network can represent, need to be specified in advance, and can not be adapted. Our goal is to allow flexible symmetry constraints that can automatically be learned from data using gradients. Learning symmetry and associated weight connectivity structures from scratch is difficult for two reasons. First, it requires efficient and flexible parameterisations of layer-wise equivariances. Secondly, symmetries act as constraints and are therefore not encouraged by training losses measuring data fit. To overcome these challenges, we improve parameterisations of soft equivariance and learn the amount of equivariance in layers by optimising the marginal likelihood, estimated using differentiable Laplace approximations. The objective balances data fit and model complexity enabling layer-wise symmetry discovery in deep networks. We demonstrate the ability to automatically learn layer-wise equivariances on image classification tasks, achieving equivalent or improved performance over baselines with hard-coded symmetry

Potato leafroll virus : molecular analysis and genetically engineered resistance

The nucleotide sequence of the genomic RNA of potato leafroll virus (PLRV) was elucidated and its genetic organization deduced (Chapter 2). Six open reading frames (ORFs) were shown to be present on the genome. Both the PLRV coat protein gene and the RNA- dependent RNA polymerase gene were identified by interviral sequence comparison. The PLRV genomic organization was shown to be highly similar to that of beet western yellows virus (BWYV) and except for the ORF1 products all PLRV and BWYV coded proteins displayed an extensive amino acid sequence homology.In order to obtain resistance following the principle of pathogen-derived resistance, the PLRV coat protein gene was placed under the control of the cauliflower mosaic virus (CaMV) 35S promoter and used to transform potato (Chapter 3). Upon analysis of the transgenic plants obtained it was shown that, although transgenic transcripts were abundantly present in the plant tissues, the presence of transgenic coat protein could not be detected. The transgenic potato plants were shown to be susceptible to PLRV infection but contained significant lower virus titers as compared to infected wild-type potato plants. To enhance the translational expression of the coat protein gene the sequences flanking the start codon were modified to a theoretically optimized context (Chapter 4). Potato plants were transformed with the altered coat protein gene and analyzed for the presence of transgenic coat protein. Despite of the induced mutations transgenic protein could not be detected. The results from inoculation experiments with PLRV were identical to those obtained with the transgenic plants containing the unaltered coat protein gene, the transgenic plants containing less viral antigen than infected wild-type plants.To investigate the role of the PLRV ORF1 product (P1) in the viral infection process and to define its intracellular location in infected plant cells, the protein was expressed in Escherichia coli and in the baculovirus expression system and used to raise an antiserurn (Chapter 5). Expression of P1 proved to be difficult, possibly due to a toxic effect imparted by the protein. Using an antiserurn raised against a recombinant P1 fusion protein, it was determined that P1 did not accumulate in infected plant tissues to detectable levels.To further investigate the function of the ORF1, its sequence was transformed into potato (Chapter 6). Surprisingly, the transgenic plants expressing detectable levels of ORF1, transcripts displayed an altered phenotype closely resembling that of virusdiseased plants. Plants expressing a modified and therefore untranslatable, version of the ORF1, sequence were phenotypically indistinguishable from wild-type control plants, indicating that the expression of the P1 protein induced virus disease-like symptoms. The transgenic potato plants containing the ORF1, sequence were analyzed for possibly acquired resistance (Chapter 7). Upon infection one plant line showed to be highly resistant while all other plant lines were susceptible to PLRV-infection similar to wild-type plants. The resistance obtained expressed itself as near immunity, only under high inoculation pressure a low percentage of the plants became infected

Identifying the determinants in the equatorial domain of Buchnera GroEL implicated in binding Potato Leafroll Virus

Luteoviruses avoid degradation in the hemolymph of their aphid vector by interacting with a GroEL homolog from the aphid's primary endosymbiotic bacterium (Buchnera sp.). Mutational analysis of GroEL from the primary endosymbiont of Myzus persicae (MpB GroEL) revealed that the amino acids mediating binding of Potato leafroll virus (PLRV; Luteoviridae) are located within residues 9 to 19 and 427 to 457 of the N-terminal and C-terminal regions, respectively, of the discontinuous equatorial domain. Virus overlay assays with a series of overlapping synthetic decameric peptides and their derivatives demonstrated that R13, K15, L17, and R18 of the N-terminal region and R441 and R445 of the C-terminal region of the equatorial domain of GroEL are critical for PLRV binding. Replacement of R441 and R445 by alanine in full-length MpB GroEL and in MpB GroEL deletion mutants reduced but did not abolish PLRV binding. Alanine substitution of either R13 or K15 eliminated the PLRV-binding capacity of the other and those of L17 and R18. In the predicted tertiary structure of GroEL, the determinants mediating virus binding are juxtaposed in the equatorial plain

A new virus infecting Myzus persicae has a genome organization similar to the species of the genus Densovirus

The genomic sequence of a new icosahedral DNA virus infecting Myzus persicae has been determined. Analysis of 5499 nt of the viral genome revealed five open reading frames (ORFs) evenly distributed in the 5' half of both DNA strands. Three ORFs (ORF1-3) share the same strand, while two other ORFs (ORF4 and ORF5) are detected in the complementary sequence. The overall genomic organization is similar to that of species from the genus Densovirus. ORFs 1-3 most likely encode the non-structural proteins, since their putative products contain conserved replication motifs, NTP-binding domains and helicase domains similar to those found in the NS-1 protein of parvoviruses. The deduced amino acid sequences from ORFs 4 and 5 show sequence similarities with the structural proteins of the members of the genus Densovirus. These data indicate that this virus is a new species of the genus Densovirus in the family Parvoviridae. The virus was tentatively named Myzus persicae densovirus. The nucleotide sequence reported in this study appears in the EMBL, GenBank and DDBJ nucleotide sequence databases under accession number AY148187

Different genes interact with particulate matter and tobacco smoke exposure in affecting lung function decline in the general population

BACKGROUND: Oxidative stress related genes modify the effects of ambient air pollution or tobacco smoking on lung function decline. The impact of interactions might be substantial, but previous studies mostly focused on main effects of single genes. OBJECTIVES: We studied the interaction of both exposures with a broad set of oxidative-stress related candidate genes and pathways on lung function decline and contrasted interactions between exposures. METHODS: For 12679 single nucleotide polymorphisms (SNPs), change in forced expiratory volume in one second (FEV(1)), FEV(1) over forced vital capacity (FEV(1)/FVC), and mean forced expiratory flow between 25 and 75% of the FVC (FEF(25-75)) was regressed on interval exposure to particulate matter >10 microm in diameter (PM10) or packyears smoked (a), additive SNP effects (b), and interaction terms between (a) and (b) in 669 adults with GWAS data. Interaction p-values for 152 genes and 14 pathways were calculated by the adaptive rank truncation product (ARTP) method, and compared between exposures. Interaction effect sizes were contrasted for the strongest SNPs of nominally significant genes (p(interaction)>0.05). Replication was attempted for SNPs with MAF<10% in 3320 SAPALDIA participants without GWAS. RESULTS: On the SNP-level, rs2035268 in gene SNCA accelerated FEV(1)/FVC decline by 3.8% (p(interaction) = 2.5x10(-6)), and rs12190800 in PARK2 attenuated FEV1 decline by 95.1 ml p(interaction) = 9.7x10(-8)) over 11 years, while interacting with PM10. Genes and pathways nominally interacting with PM10 and packyears exposure differed substantially. Gene CRISP2 presented a significant interaction with PM10 (p(interaction) = 3.0x10(-4)) on FEV(1)/FVC decline. Pathway interactions were weak. Replications for the strongest SNPs in PARK2 and CRISP2 were not successful. CONCLUSIONS: Consistent with a stratified response to increasing oxidative stress, different genes and pathways potentially mediate PM10 and tobac smoke effects on lung function decline. Ignoring environmental exposures would miss these patterns, but achieving sufficient sample size and comparability across study samples is challengin

A tree-based decision model to support prediction of the severity of asthma exacerbations in children

This paper describes the development of a tree-based decision model to predict the severity of pediatric asthma exacerbations in the emergency department (ED) at 2 h following triage. The model was constructed from retrospective patient data abstracted from the ED charts. The original data was preprocessed to eliminate questionable patient records and to normalize values of age-dependent clinical attributes. The model uses attributes routinely collected in the ED and provides predictions even for incomplete observations. Its performance was verified on independent validating data (split-sample validation) where it demonstrated AUC (area under ROC curve) of 0.83, sensitivity of 84%, specificity of 71% and the Brier score of 0.18. The model is intended to supplement an asthma clinical practice guideline, however, it can be also used as a stand-alone decision tool

Strange Quark Matter and Compact Stars

Astrophysicists distinguish between three different types of compact stars. These are white dwarfs, neutron stars, and black holes. The former contain matter in one of the densest forms found in the Universe which, together with the unprecedented progress in observational astronomy, make such stars superb astrophysical laboratories for a broad range of most striking physical phenomena. These range from nuclear processes on the stellar surface to processes in electron degenerate matter at subnuclear densities to boson condensates and the existence of new states of baryonic matter--like color superconducting quark matter--at supernuclear densities. More than that, according to the strange matter hypothesis strange quark matter could be more stable than nuclear matter, in which case neutron stars should be largely composed of pure quark matter possibly enveloped in thin nuclear crusts. Another remarkable implication of the hypothesis is the possible existence of a new class of white dwarfs. This article aims at giving an overview of all these striking physical possibilities, with an emphasis on the astrophysical phenomenology of strange quark matter. Possible observational signatures associated with the theoretically proposed states of matter inside compact stars are discussed as well. They will provide most valuable information about the phase diagram of superdense nuclear matter at high baryon number density but low temperature, which is not accessible to relativistic heavy ion collision experiments.Comment: 58 figures, to appear in "Progress in Particle and Nuclear Physics"; References added for sections 1,2,3,5; Equation (116) corrected; Figs. 1 and 58 update