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J R de Miranda

Publications and source records attributed to J R de Miranda.

14 recordsLinked to original sources
PubMed2004

Complete nucleotide sequence of Kashmir bee virus and comparison with acute bee paralysis virus.

The complete nucleotide sequence of a novel virus is presented here together with serological evidence that it belongs to Kashmir bee virus (KBV). Analysis reveals that KBV is a cricket paralysis-like virus (family Dicistroviridae: genus Cripavirus), with a non-structural polyprotein open reading frame in the 5' portion of the genome separated by an intergenic region from a structural polyprotein open reading frame in the 3' part of the genome. The genome also has a polyadenylated tail at the 3' terminus. KBV is one of several related viruses that also includes acute bee paralysis virus (ABPV). Although KBV and ABPV are about 70 % identical over the entire genome, there are considerable differences between them in significant areas of the genome, such as the 5' non-translated region (42 % nucleotide identity), between the helicase and 3C-protease domains of the non-structural polyprotein (57 % amino acid identity) and in a 90 aa stretch of the structural polyprotein (33 % amino acid identity). Phylogenetic analyses show that KBV and ABPV isolates fall into clearly separated clades with moderate evolutionary distance between them. Whether these genomic and evolutionary differences are sufficient to classify KBV and ABPV as separate species remains to be determined.

5' Untranslated Regions↗
PubMed2001

Phylogenetic placement of a novel tenuivirus from the grass Urochloa plantaginea.

Evidence is presented that a tenuivirus recovered from the grass Urochloa plantaginea is probably a novel tenuivirus species, to be called Urochloa hoja blanca virus (UHBV). It is related to both Echinochloa hoja blanca virus (EHBV) and Rice hoja blanca virus (RHBV), and these three form a group distinct from Maize stripe virus (MStV) and Rice stripe virus (RStV). Phylogenetic analysis of the sequence data for RNA-3 and RNA-4 of these viruses supports the hypothesis that EHBV and UHBV may have evolved from an ancestral form of RHBV, precipitated by the introduction of Echinochloa colona and Urochloa plantaginea to America.

Phylogeny↗
PubMed1997

Comparison of Colombian and Costa Rican strains of rice hoja blanca tenuivirus.

The sequences of RNA-3 and RNA-4 of rice hoja blanca tenuivirus isolates from Colombia and from Costa Rica were determined and analyzed. These isolates were 98.9% and 98.6% identical in the coding and non-coding regions of RNA-3, and 96.9 and 91.5% identical in the coding and non-coding regions of RNA-4, and are therefore strains of the same virus. There is about three times as much variation between isolates (based on consensus sequences) as there is within isolates (based on sequences of individual clones). There is also considerably more variation for RNA-4 (both between and within isolates) than there is for RNA-3, even though between tenivirus species RNA-3 has diverged more than RNA-4, implying that the evolution of the tenuivirus RNAs is not necessarily dependent on the amount of variation found for these RNAs.

Colombia↗
PubMed1996

Sequence of echinochloa hoja blanca tenuivirus RNA-5.

The sequence is presented of RNA-5 of Echinochloa hoja blanca tenuivirus, a second tenuivirus associated with rice cultivation in Latin America (after rice hoja blanca virus). The RNA is 1334 nucleotides long and contains in the complementary sense RNA a single long open reading frame. The deduced amino acid sequence of this open reading frame shows that it encodes a highly basic and hydrophilic 44 kD protein (pc5) with about 50% similarity to the pc5 protein of maize stripe virus (MStV). This and other features of the RNA are discussed.

Amino Acid Sequence↗
PubMed1996

Sequence of Echinochloa hoja blanca tenuivirus RNA-4.

The sequence is presented of RNA-4 of Echinochloa hoja blanca tenuivirus (EHBV), one of two tenuiviruses associated with rice cultivation in Latin America (together with rice hoja blanca virus; RHBV). Analysis of the sequence shows that the coding regions of EHBV RNA-4 are closely related to those of RHBV RNA-4. However, the intergenic region separating the two ambisense open reading frames, are highly distinct for the two viruses. The features of the RNA and the comparisons with the sequences of RNA-4 of RHBV, rice stripe virus (RStV) and maize stripe virus (MStV) are discussed.

Amino Acid Sequence↗
PubMed1996

Sequence of Echinochloa hoja blanca tenuivirus RNA-3.

Analysis of the sequence of the 2336 nucleotide RNA-3 of Echinochloa hoja blanca tenuivirus shows that it is closely related to RNA-3 of rice hoja blanca tenuivirus, the principal virus disease of rice in Latin America. This is especially true for the coding regions, where the viruses are almost 90% similar. However, the non-coding regions of RNA-3 of these viruses, principally the intergenic region separating the two ambisense open reading frames, are only about 50% similar, suggesting that these are distinct viruses. The results closely resemble those obtained for the analysis of RNA-4 of these viruses, both in the absolute and relative percentage similarities of the coding and non-coding regions. This implies a coordinated evolution of the different tenuivirus RNA segments. The features of the RNA and the comparisons with the sequences of RNA-3 of RHBV, rice stripe virus (RStV) and maize stripe virus (MStV) are discussed.

Amino Acid Sequence↗
PubMed1996

Rapid, small scale purification of rice hoja blanca and Echinochloa hoja blanca tenuivirus ribonucleoprotein.

Highly purified tenuivirus ribonucleoprotein was obtained from small amounts of leaf tissue by sedimenting the ribonucleoprotein particles from debris-free plant extract into a 30% sucrose cushion, in 1.5-mL microfuge tubes. Using this protocol, significant size differences were discovered in the double-stranded forms of the viral genomic RNAs of rice hoja blanca tenuivirus and a tenuivirus isolated from Echinochloa colonum, a common weed of rice cultivation.

Oryza↗
PubMed1995

Sequence comparison and classification of beet luteovirus isolates.

Three distinct sequence groups were found among partial nucleotide sequences of 38 isolates of beet western yellows virus (BWYV) and beet mild yellowing virus (BMYV) from Europe, Iran and the USA. The first group contains both sugar beet and oilseed rape specific isolates, and the differentiating characteristic linked to this host range specificity are 2 single base pair changes in a 1,200 nucleotide region of the genome. It is proposed that the European BWYV strains that can be transferred at low frequency between rape and sugar beet belong to this group. Also belonging to this group are the published BWYV sequences of Veidt et al. and of the California BWYV-ST9 isolate. The second group contains mostly rape-derived isolates which have an intergenic region highly distinct from that of group-1 isolates but similar polymerase and coat protein regions. It is proposed that the rape-specific BWYV isolates which cannot be transmitted to sugar beet belong to this group. The third group contains mostly beet-specific isolates from Southern Europe and Iran, and may be adapted to the Mediterranean climate and flora. It is distinct from groups 1 and 2 in all three genome regions investigated and its polymerase and intergenic regions are as much related to those of potato leafroll virus (PLRV) and curcurbit aphid borne yellows virus (CABYV) as they are to those of group-1 and group-2. On the basis of sequence similarities and established nomenclature it is proposed to use BWYV for groups 1 and 2 (BWYV-1 and BWYV-2 respectively) and to use BMYV for group-3 isolates, which are distinct enough from the other two groups to merit a separate nomenclature.

Amino Acid Sequence↗
PubMed1990

Metallothionein genes from the flowering plant Mimulus guttatus.

In response to excess metal, higher plants produce metal-binding peptides [( gamma EC]nG) whose biosynthesis is believed to be mediated by enzymes involved in glutathione (gamma ECG) metabolism. In contrast, animals synthesize metallothioneins, gene-encoded low molecular weight cysteine-rich metal-binding proteins. In an investigation of copper-regulated genes in the copper-tolerant flowering plant Mimulus guttatus, we have isolated a series of cDNA clones identifying two genes which encode a protein with class I metallothionein domains. This represents the first description of a metallothionein gene in a flowering plant.

Cloning, Molecular↗
PubMed1989

Analysis of dominance for competitive ability in Drosophila melanogaster.

In these experiments the genetic basis of larval competition in Drosophila melanogaster was investigated. Competitive ability was defined by a series of regression coefficients relating larval performance to their mono- and duo-culture densities. Sixteen inter-related F1 hybrids were individually compared with their parents, revealing the presence of large amounts of dominance and heterosis for the various competitive parameters, all directed towards improved competitive ability. Analysis of the F1 hybrids amongst themselves revealed that most of the heterosis was due to either interchromosomal interaction, or the complementing action of haploid autosomes and relatively little was due to any specific interaction between the homologues. The relevance of these results to the current understanding of heterosis is discussed.

Animals↗
PubMed1988

Genetic analysis of larval competition in Drosophila melanogaster.

A chromosome assay was employed to determine the genetic basis of the competitive ability of the larvae of Drosophila melanogaster when competing for a controlled amount of food. The effects of increasing stress due to intra- and inter-genotypic competition were analysed using a yield-density regression analysis producing estimates of the absolute performance at a standard reference density (e-values), the magnitude of intra-genotypic competition and the inter-genotypic competitive effect of one genotype on another. A distinction was made between the Sensitivity and the Pressure components of inter-genotypic competition. The probability of survival and mean adult weight were used as measures of competitive success. The genetic analysis revealed high levels of heterosis for the e-values and inter-genotypic pressure, with correspondingly high inter-chromosomal interactions. Inter-genotypic sensitivity was less consistently heterotic and less epistatic. All dominance was directed towards a competitively superior genotype and both major autosomes were involved in the determination of competitive ability with the greater effect residing on the third chromosome. There was evidence of early non-competitive larval mortality in one of the two sets of substitution lines investigated and the effect of this on the estimation of the genetic parameters is discussed.

Animals↗
PubMed1988

Larval competition in Drosophila melanogaster. I. Estimation of larval growth parameters.

Despite extensive research into the competitive interactions between the larvae of Drosophila for food, there have been few studies of the biological characteristics of the larvae which might underly competition. Here we present a sensitive method for estimating the larval feeding rate, larval gut capacity, larval conversion efficiency and larva-adult conversion efficiency, using radioactively labelled yeast. Two developmental stages, defined by the time since oviposition, were investigated in eight genetically distinct strains of Drosophila melanogaster. Significant genetic variation was recovered for all parameters at the second instar but only for conversion efficiency at the third instar. Feeding rate and the gut capacity had large and heterogenous error variances, especially in the third instar, while conversion efficiencies were relatively more stable.

Animals↗
PubMed1988

Larval competition in Drosophila melanogaster. II. Comparing biological and competitive parameters.

Recent developments in the analysis of density dependent competition in Drosophila melanogaster have identified two distinct parameters, namely the competitive pressure or aggression exerted by a genotype and the sensitivity or response of a genotype to such aggression. Assuming that response is more related to the efficiency of utilising available resources and aggression to the ability to acquire those resources, we attempt to relate estimates of aggression and response obtained from a range of genotypes to estimates of larval feeding rates and conversion efficiencies. No significant correlations were found and we conclude that other characteristics must be involved in a more complex determination of competitive ability.

Animals↗