Vocal behaviour reveals asymmetries in neighbour relationships in a semi-colonial raptor, the Eurasian Scops Owl Otus scops

Territorial animals often reduce aggression towards familiar neighbours compared to unfamiliar conspecifics. However, variation in the response to different neighbours is less known. In this work, I examined the territorial behaviour of male scops owls during countersinging interactions with two familiar neighbours and I asked whether vocal behaviour of the focal male reflected dear-enemy relationships. Analysis revealed that the focal male’s vocal frequency was associated with (1) the degree of instability of the territory boundary shared with a neighbour and (2) the motivation to persist in the dyadic interaction with that neighbour. Patterns of movement directed to specific individuals suggest that scops owls do discriminate between neighbours. A case of partial territory takeover was observed that was accompanied by temporal changes in vocal frequency in one of the opponents, confirming that vocal frequency is a flexible, context-dependent feature of the relationship of neighbouring scops owls.

Measuring Behavior in the Home Cage: Study Design, Applications, Challenges, and Perspectives

The reproducibility crisis (or replication crisis) in biomedical research is a particularly existential and under-addressed issue in the field of behavioral neuroscience, where, in spite of efforts to standardize testing and assay protocols, several known and unknown sources of confounding environmental factors add to variance. Human interference is a major contributor to variability both within and across laboratories, as well as novelty-induced anxiety. Attempts to reduce human interference and to measure more "natural" behaviors in subjects has led to the development of automated home-cage monitoring systems. These systems enable prolonged and longitudinal recordings, and provide large continuous measures of spontaneous behavior that can be analyzed across multiple time scales. In this review, a diverse team of neuroscientists and product developers share their experiences using such an automated monitoring system that combines Noldus PhenoTyper® home-cages and the video-based tracking software, EthoVision® XT, to extract digital biomarkers of motor, emotional, social and cognitive behavior. After presenting our working definition of a "home-cage", we compare home-cage testing with more conventional out-of-cage tests (e.g., the open field) and outline the various advantages of the former, including opportunities for within-subject analyses and assessments of circadian and ultradian activity. Next, we address technical issues pertaining to the acquisition of behavioral data, such as the fine-tuning of the tracking software and the potential for integration with biotelemetry and optogenetics. Finally, we provide guidance on which behavioral measures to emphasize, how to filter, segment, and analyze behavior, and how to use analysis scripts. We summarize how the PhenoTyper has applications to study neuropharmacology as well as animal models of neurodegenerative and neuropsychiatric illness. Looking forward, we examine current challenges and the impact of new developments. Examples include the automated recognition of specific behaviors, unambiguous tracking of individuals in a social context, the development of more animal-centered measures of behavior and ways of dealing with large datasets. Together, we advocate that by embracing standardized home-cage monitoring platforms like the PhenoTyper, we are poised to directly assess issues pertaining to reproducibility, and more importantly, measure features of rodent behavior under more ethologically relevant scenarios.

HFpEF score discriminates severity of cardiovascular profile in asymptomatic treated hypertensive patients: the campania salute network

Background

The heart failure with preserved ejection fraction (HFpEF) score is easy to use and potentially useful to discriminate HFpEF from noncardiac causes of dyspnea. HFpEF score may be expressed also as probability to have HFpEF.

Purpose

We investigated whether a high HFpEF score can identify specific cardiovascular (CV) profile in treated hypertensive patients even without dyspnea.

Methods

From September to December 2019, we consecutively enrolled treated hypertensive patients without dyspnea, with normal left ventricular (LV) ejection fraction (>50%), and chronic kidney disease of no more than stage III. In addition to standard echocardiographic parameters we evaluated: 1) inappropriate LV mass, identified as a percent of predicted LV mass >128%, 2) myocardial energetic efficiency as the ratio of stroke volume to heart rate normalized by LV mass (MEEi), and 3) an estimate of arterial stiffness, i.e. the ratio of pulse pressure and stroke index (by allometric normalization by height), as previously reported. The probability of HFpEF was calculated from the HFpEF score, using body mass index, pulmonary systolic pressure, mitral E/E' ratio, age, and history or evidence of atrial fibrillation.

Results

188 patients with complete data were analyzed (42% women, age 61±14 years, 9% diabetic). Patients were then divided into 3 groups according to HFpEF probability tertiles and compared by ANOVA and trend analysis (Table 1).

Conclusions

Probability of HFpEF using HFpEF score and non-standard echocardiographic parameters identify worse CV profile in treated hypertensive patients without dyspnea.

Funding Acknowledgement

Type of funding source: None

Industrial scale bio-detoxification of raw olive mill wastewaters by the use of selected microbial yeast and bacterial strains to obtain a new source for fertigation

The Olive Mill Wastewaters (OMWs) are one of the most important agro-industrial wastes of the Mediterranean Countries and the disposal by draining them onto land has been proved to be damaging for soils, plants and groundwater due to their polluting power. The present report describes a new method for bio-detoxification of undiluted fresh OMW based on the driven selection of aerobic yeasts and bacteria. The identified yeast Candida boidinii A5y and the bacterium Paenibacillus albidus R32b strains allowed the treatment of freshly produced raw OMW characterized by very high COD value and phenolic content, when applied as sequential inoculum. The treated OMW showed the absence of antimicrobial effects and a strongly reduction of phytotoxic activity on the germination of several plant seeds. The process was successfully validated on an industrial scale without any pre-treatment, dilution and/or supplementation of the raw waste. Bio-detoxified OMW produced by this sustainable and low-cost process would be suitable for new non-chemical fertigation or soilless applications. The described procedure represents a virtuous example of circular economy efficaciously applied for a depleting agri-food resource.

Sleep-disordered breathing and epicardial adipose tissue in patients with heart failure

BACKGROUND AND AIMS

Sleep-disordered breathing (SDB) is common in patients with heart failure (HF), contributes to the progression of cardiac disease, and is associated with adverse prognosis. Previous evidence indicates that epicardial adipose tissue (EAT) is independently associated with sleep apnea in obese individuals. We explored the relationship between SDB and EAT in HF patients.

METHODS AND RESULTS

EAT thickness was assessed by echocardiography in 66 patients with systolic HF undergoing nocturnal cardiorespiratory monitoring. A significantly higher EAT thickness was found in patients with SDB than in those without SDB (10.7 ± 2.8 mm vs. 8.3 ± 1.8 mm; p = 0.001). Among SDB patients, higher EAT thickness was found in both those with prevalent obstructive sleep apnea (OSA) and those with prevalent central sleep apnea (CSA). Of interest, EAT thickness was significantly higher in CSA than in OSA patients (11.9 ± 2.9 vs. 10.1 ± 2.5 p = 0.022). Circulating plasma norepinephrine levels were higher in CSA than in OSA patients (2.19 ± 1.25 vs. 1.22 ± 0.92 ng/ml, p = 0.019). According to the apnea-hypopnea index (AHI), patients were then stratified in three groups of SDB severity: Group 1, mild SDB; Group 2, moderate SDB; Group 3, severe SDB. EAT thickness progressively and significantly increased from Group 1 to Group 3 (ANOVA p < 0.001). At univariate analysis, only left ventricular ejection fraction and AHI significantly correlated with EAT (p = 0.019 and p < 0.0001, respectively). At multivariate analysis, AHI was the only independent predictor of EAT (β = 0.552, p < 0.001).

CONCLUSIONS

Our results suggest an association between the presence and severity of sleep apneas and cardiac visceral adiposity in HF patients.

A 3D analysis of flight behavior of Anopheles gambiae sensu stricto malaria mosquitoes in response to human odor and heat

Female mosquitoes use odor and heat as cues to navigate to a suitable landing site on their blood host. The way these cues affect flight behavior and modulate anemotactic responses, however, is poorly understood. We studied in-flight behavioral responses of females of the nocturnal malaria mosquito Anopheles gambiae sensu stricto to human odor and heat. Flight-path characteristics in a wind tunnel (flow 20 cm/s) were quantified in three dimensions. With wind as the only stimulus (control), short and close to straight upwind flights were recorded. With heat alone, flights were similarly short and direct. The presence of human odor, in contrast, caused prolonged and highly convoluted flight patterns. The combination of odor+heat resulted in longer flights with more landings on the source than to either cue alone. Flight speed was greatest (mean groundspeed 27.2 cm/s) for odor+heat. Odor alone resulted in decreased flight speed when mosquitoes arrived within 30 cm of the source whereas mosquitoes exposed to odor+heat maintained a high flight speed while flying in the odor plume, until they arrived within 15 cm of the source. Human odor evoked an increase in crosswind flights with an additive effect of heat at close range (<15 cm) to the source. This was found for both horizontal and vertical flight components. However, mosquitoes nevertheless made upwind progress when flying in the odor+heat generated plume, suggesting that mosquitoes scan their environment intensively while they progress upwind towards their host. These observations may help to improve the efficacy of trapping systems for malaria mosquitoes by (1) optimizing the site of odor release relative to trap entry and (2) adding a heat source which enhances a landing response.

Selection of non-conventional yeasts and their use in immobilized form for the bioremediation of olive oil mill wastewaters

The yeast population dynamics in olive wastewaters (OMW), sampled in five mills from Salento (Apulia, Southern Italy), were investigated. Three hundred yeasts were isolated in five industrial mills and identified by molecular analysis. Strains belonging to Geotrichum, Saccharomyces, Pichia, Rhodotorula and Candida were detected. Five G. candidum strains were able to grow in OMW as the sole carbon source and to reduce phenolics, chemical oxygen demand (COD) and antimicrobial compounds. One G. candidum isolate was selected for whole-cell immobilization in calcium alginate gel. The COD and phenolic reduction obtained with immobilized cells showed a 2.2- and 2-fold increase compared to the removal obtained with free cells, respectively. The immobilization system enhanced yeast oxidative activity by avoiding the presence of microbial protease in treated OMW. To our knowledge, this is the first report on G. candidum whole-cell immobilization for OMW bioremediation.

Technological properties of Oenococcus oeni strains isolated from typical southern Italian wines

AIMS

To isolate indigenous Oenococcus oeni strains suitable as starters for malolactic fermentation (MLF), using a reliable polyphasic approach.

METHODS AND RESULTS

Oenococcus oeni strains were isolated from Nero di Troia wines undergoing spontaneous MLF. Samples were taken at the end of alcoholic fermentation and during MLF. Wine samples were diluted in a sterile physiological solution and plated on MRS and on modified FT80. Identification of O. oeni strains was performed by a polymerase chain reaction (PCR) experiment using strain-specific primers. Strains were further grouped using a multiplex RAPD-PCR analysis. Then, six strains were inoculated in two winelike media with two different ethanol concentrations (11 and 13% vol / vol) with a view to evaluate their capacity to grow and to perform MLF. In addition, a quantitative PCR (qRT-PCR) approach was adapted to monitor the physiological state of the strains selected.

CONCLUSION

A positive correlation between the malolactic activity performance and the ability to develop and tolerate stress conditions was observed for two selected O. oeni strains.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results reported are useful for the selection of indigenous MLF starter cultures with desired oenological traits from typical regional wines. It should be the base for the improvement in organoleptic quality of typical red wine.

The role of the C-terminal region of olive latent virus 1 coat protein in host systemic infection

A full-length cDNA clone of olive latent virus 1 (OLV-1), a member of the genus Necrovirus, family Tombusviridae, was subjected to site-directed mutagenesis, and coat protein gene mutants were constructed. A mutant clone, denoted Delta3297, was obtained by deleting the nucleotide in position 3297, thus inducing a frameshift and replacing the last 49 amino acids of the viral coat protein (CP) by a shorter sequence of 39 amino acids. This mutant was viable, stable, able to synthesize a smaller CP, and able to give rise to the formation of apparently intact virus particles. Cell-to-cell movement of Delta3297 in Nicotiana benthamiana leaves was not affected, but, contrary to wild type OLV-1, it failed to spread systemically. These results indicate that virion formation is necessary but not sufficient for long-distance movement for OLV-1 and highlights the role of the CP carboxy-terminal domain in systemic infection.

Subcellular localization and immunodetection of movement proteins of olive latent virus 1

Polyclonal sera raised to Escherichia coli-expressed movement proteins encoded by ORF 3 (p8K) and ORF 4 (p6K) of olive latent virus 1, were used for their immunodetection in infected Nicotiana benthamiana plants. In subfractionated locally infected tissues 4 days post inoculation (d.p.i.) that were analysed by Western blot, p8K was found in the fast-sedimenting fractions P1 and P30 containing membranous material and/or cell organelles and, likely, the fibrous structures mentioned below, but not in the soluble protein-containing supernatant. No p6K could be detected in these extracts. In locally inoculated leaves p8K began to accumulate from 2 d.p.i onwards reaching its peak at 4 d.p.i. Intracellular immunogold labelling of cells from locally and systemically infected tissues localized p8K primarily in fibrous inclusions made up of thin filaments with a helical structure present in the cytoplasm of locally and systemically infected cells. In systemic infections a light and scattered labelling was observed in the cytoplasm and near the cell wall. The specific serum to p6K did not label the fibrous structures and failed to recognize its antigen in systemically and locally infected tissues except at 4 d.p.i., when scattered labelling was observed in the cytoplasm and near plasmodesmata.

Persistence of fenitrothion in oranges and clementines after treatment with emulsifiable concentrate and microencapsulate formulations

The rate of decline of fenitrothion residues was investigated in oranges and clementines after treatment with two different kinds of commercial formulations: emulsifiable concentrate (Afidina M) and microencapsulate (Fenitrocap and IPM 400). The study was performed on the fruit and leaves over 131 and 161 days for oranges, and over 78 and 86 days for clementines, respectively. In fruit, the experimental data showed a similar behaviour of the active ingredient for both kinds of commercial formulations. High mean levels of fenitrothion (between about 0.4 and 0.8 mg kg(-1)) were persistent for at least 75 days after treatment in oranges and 50 days in clementines, with statistically significant declines observed only at days 110 and 78, respectively. A rapid decline of fenitrothion levels was observed in orange and clementine leaves during the starting phase followed by a slower decrease during the later stage; the decline was more pronounced with the treatment of emulsifiable concentrates. These findings are indicative of a poor degradability of fenitrothion in citrus fruits, and suggest that repeated or uneven applications of the pesticide should be avoided in order to exclude the risk of exceeding the maximum residue level permitted by the current regulations.

Characterization of Saccharomyces cerevisiae strains isolated from must of grape grown in experimental vineyard

AIMS

Isolation and characterization of indigenous Saccharomyces cerevisiae strains from 12 grape varieties grown in an experimental vineyard of Apulia.

METHODS AND RESULTS

Thirty to 40 colonies from each of the 12 fermentations were obtained at the end stage of spontaneous fermentation. By using morphological and physiological methods and by the PCR analysis of internal transcribed ITS1-5,8S-ITS2, the isolates belonging to Saccharomyces genus were identified. These isolates were further characterized by amplification with S. cerevisiae species- and delta element-specific primers, thus allowing the identification of S. cerevisiae strains selected from each of the 12 fermentations. By means of RFLP analysis of mtDNA, each S. cerevisiae population isolated from a single fermentation appeared to constitute a genetically homogenous group. The comparison of the 12 cultivar-specific mtDNA RFLP patterns, allowed classifying the 12 S. cerevisiae populations into three genetically homogenous groups. The isolated strains fermented vigorously in synthetic and grape juice medium and showed high alcohol and sulphur dioxide (SO(2)) resistance and low hydrogen sulphite (H(2)S) production.

CONCLUSIONS

The molecular analysis, in conjunction with the traditional morphological and physiological methods, was useful in discriminating at strain level the indigenous population of S. cerevisiae present in a vineyard of Apulia. The dominant S. cerevisiae strains identified in the 12 fermented musts showed potentially important oenological characteristics.

SIGNIFICANCE AND IMPACT OF THE STUDY

The characterization of natural S. cerevisiae strains from several typical Italian grapes grown in a restricted experimental vineyard is an important step towards the preservation and exploitation of yeast biodiversity of Apulia, a relevant wine-producing region. The close relationship between the S. cerevisiae strains from different grapes grown in the same vineyard indicated that the occurrence of native strains is representative of the area rather than of the variety of grapes.

Evidence for the effect of learning on timing of reproduction in blue tits

We experimentally show that in blue tits (Parus caeruleus) egg-laying date is causally linked to experience in the previous year. Females that received additional food in the nestling period in one year laid eggs later in the next year compared with the control birds, whatever the degree of synchronization with the natural food abundance in the previous year. As a result, they raised their brood much later than the peak period of nestling food availability in the next year. The response to experience is adaptive for blue tits, which live in heterogeneous habitats where the peak period of food varies, but once settled will breed at the same location for life.

Complete nucleotide sequence of RNA-2 of Olive latent ringspot virus

The complete nucleotide sequence of Olive latent ringspot virus (OLRSV) RNA-2 was determined. This RNA is 3969 nucleotides in length and contains a single open reading frame of 3448 nt, that encodes a polypeptide of 1146 amino acids, with a calculated Mr of 126,044. OLRSV RNA-2 has a structural organization typical of nepoviruses, with the coat protein (CP) cistron located in the C-terminal and the putative movement protein (MP) in the N-terminal regions of the polyprotein. Computer-assisted comparison of coat proteins of OLRSV and other nepoviruses disclosed relationships that tally with subgrouping based on physicochemical properties.

Synthesis of infectious transcripts of olive latent virus 1: genes required for RNA replication and virus movement

Genomic RNA of olive latent virus 1 (OLV-1) contains five open reading frames (ORFs) encoding proteins of 23, 82, 8, 6 and 30 (CP) kDa. A full-length cDNA copy of OLV-1RNA was prepared and cloned in a low-copy-number vector (pMUC-19) downstream of or T7 RNA polymerase promoter. Transcripts derived from this template, denoted pMUC-OLV, were highly infectious when inoculated in local and systemic hosts and infected tissues contained virus-like particles. Genes required for replication and virus movement were mapped by site-directed and deletion mutogenesis of the pMUC-OLV. ORF1 and ORF2 mutants were not viable, suggesting that replication requires the 23 and 82 kDa proteins. The 8 and 6 kDa polypeptides were involved in cell-to-cell movement, since their absence did not interfere with RNA replication but prevented systemic infection of inoculated plants. Mutant clones in R and S domains of the CP gene could replicate, but they did not systemically infect Nicotiana benthamiana, indicating that the CP gene is required for OLV-1 long-distance translocation. Mutant clones with large deletions in the CP gene were not viable, probably due to loss of 3'-proximal sequences required for RNA replication.

Subcellular localization and in vivo identification of the putative movement protein of olive latent virus 2

The gene encoding the 36.5 kDa ('36K') nonstructural protein located on RNA3 of olive latent virus 2 (OLV-2) was cloned, expressed with the Escherichia coli pGEX-2T system and the purified protein used to raise a polyclonal antiserum. Immunoblot analysis of OLV-2-infected Nicotiana benthamiana plants showed that the 36K protein accumulated in the early stages of infection and was associated with a subcellular fraction enriched in cytoplasmic membranes. In infected cells there were tubular structures, some containing virus-like particles, scattered in the cytoplasm or protruding from or penetrating the cell wall at the plasmodesmata. Immunogold labelling localized the 36K protein in the plasmodesmata of OLV-2-infected cells and showed it to be associated with virus-containing tubules. Leaf trichome cells of N. tabacum plants, transformed with a 36K-green fluorescent protein (GFP) fusion construct, revealed localized fluorescence in the cell walls, possibly due to association of the fusion protein with plasmodesmata. When the same 36K-GFP fusion protein was expressed in N. tabacum protoplasts, long tubular fluorescent structures protruded from the protoplast surface, suggesting that the 36K protein is responsible for tubule induction. The conclusion is drawn that this protein is likely to be the OLV-2 movement protein, mediating cell-to-cell virus movement, and that movement is by a tubule-guided mechanism.

Oleavirus, a new genus in the family Bromoviridae

Oleavirus is a monotypic genus having olive latent virus 2 (OLV-2) as the type species. OLV-2 is transmitted by inoculation of sap but not by aphids. Virus particles have different shape and size, ranging from quasi spherical to bacilliform with length of 37, 43, 48, and 55 nm, respectively, and a diameter of ca. 18 nm. Virions do not contain lipids or carbohydrates and possess a single coat protein species with molecular mass of ca. 24 kDa, which is not required for infectivity. Individual particles contain a single molecule of linear, positive sense ssRNA, constituting ca. 19% of their weight. The genome consists of three functional non polyadenylated, capped, positive sense, single-stranded RNA molecules occurring as three functional species of 3126 nt (RNA1, monocistronic), 2734 nt (RNA2, monocistronic), and 2438 nt (RNA3, bicistronic). Virions encapsidate a fourth RNA species 2078 nt in size (RNA4) with no apparent messenger activity. Virus replication is thought to occur in the cytoplasm possibly in connection with vesicular structures. The strategy of replication encompasses proteolytic processing and subgenomic RNA production. Oleavirus does not have a complete straightforward relationship with any of the current genera in the Bromoviridae, but shows homologies in diverging directions with one genus of the family or another.

Evolutionary dynamics of cucumber mosaic virus satellite RNA during natural epidemics in Italy

The evolutionary dynamics of 22 variants of cucumber mosaic virus satellite RNA (CMV satRNA) isolated in Italy during virus epidemics from 1988 to 1993 were investigated on the basis of their primary structure and biological properties. Most of the variants were amplified from total nucleic acid preparations extracted from field-infected plants, thus representing wild isolates of CMV satRNA. Eleven variants were associated with subgroup II CMV strains, 10 with subgroup I and 1 with a mixed infection by both strains. When inoculated onto tomato seedlings, the variants induced the phenotype (necrogenic or ameliorative) predicted by their nucleotide sequence. Phylogenetic relationships between the satRNA variants were determined using the stationary Markov model, a stochastic model for evolution. For each satRNA, the Markov analysis gave a good correlation between position in the phylogenetic tree and biological properties. The variants with ameliorative and necrogenic phenotypes in tomato followed two different evolutionary dynamics in nature. Tfn-satRNA, a 390-nt-long molecule, followed a third type of evolutionary dynamic far apart from that of the shorter satRNA molecules (i.e., those in the 334- to 340-nt-length class). Average values of the mean constant rate of nucleotide substitutions/site (Ksubs/site) indicated that in nature the variants tend to keep their heterogeneity unchanged from one epidemic episode to the other, even if the outbreaks occur in places very far from each other. This seems to be in agreement with the proposed maintenance of a functional molecular structure as a constraint to CMV satRNA evolution.

The nucleotide sequence of RNA1 and RNA2 of olive latent virus 2 and its relationships in the family Bromoviridae

The complete nucleotide sequence of RNA1 and RNA2 of olive latent virus 2 (OLV-2), a virus with quasi-spherical to bacilliform particles and a non-polyadenylated tripartite ssRNA genome, was determined. RNA1 consists of 3126 nucleotides and contains a single open reading frame (ORF) coding for a polypeptide with a molecular mass of 102689 Da (p1a). RNA2 is also a monocistronic molecule, 2734 nt in length, coding for a polypeptide with a molecular mass of 90631 Da (p2a). The translation products of RNA1 and RNA2 possess the motifs proper to helicase, methyltransferase (RNA1) and RNA polymerase (RNA2), suggesting that both are involved in the replication of the viral RNA. The similarities found between OLV-2 and members of the Bromoviridae in some properties and in the sequences of all genomic products (including p1a and p2a) are strongly indicative that it belongs in this family. OLV-2, however, did not show a direct relationship with any of the current genera in the family. Rather, it revealed homologies in diverging directions with one or other of the Bromoviridae genus, thus qualifying as the possible representative of a new taxon in this family.

Nucleotide sequence of the genome of a citrus isolate of olive latent virus 1

The 3699 nt genome of olive latent virus 1 (OLV-1), described years ago from Southern Italy as a putative sobemovirus, was completely sequenced. OLV-1 genomic RNA was not polyadenylated and had a structure virtually identical to that of species of the Necrovirus rather than the Sobemovirus genus. Five open reading frames (ORFs) were identified, of which the 5'-proximal encoded a 23K protein and ended with an amber codon whose readthrough could yield a putative 82K product. This polypeptide had extensive sequence similarity with polymerases of serotypes A and D of tobacco necrosis necrovirus (TNV-A and TNV-D) and species of the family Tombusviridae and related genera (Dianthovirus and Machlomovirus). Two small ORFs followed, which encoded polypeptides of 8K and 6K, respectively. The 6K product had extensive homology with the comparable 6K protein of TNV-A and was also related to the 11K protein of shallot latent carlavirus, one of the "triple block" polypeptides involved in cell-to-cell virus movement. The 3'-proximal ORF was in the same position as the coat protein (CP) cistron of necroviruses and encoded a 30K product related to CP of both TNV-A and -D. Computer-assisted comparative analysis of structural and non-structural proteins of OLV-1, TNV-A and TNV-D disclosed on overall distant relationship between OLV-1 and TNV-D. OLV-1 genome appeared homologous to that of TNV-A, but differences from TNV-A were the absence of the small ORF downstream of the CP cistron and in the low degree of sequence identity in CP (39% aa identity). OLV-1 is serologically distantly related to TNV-A and even more distantly related to TNV-D. We propose that OLV-1 is a necrovirus species in its own right.

The nucleotide sequence of RNA3 and RNA4 of olive latent virus 2

Olive latent virus 2 (OLV2), a virus with particle shapes resembling those of alfalfa mosaic alfamovirus (AMV), has four major RNA species, two of which (RNA3 and RNA4) were completely sequenced. RNA3 was a bicistronic molecule containing two clear-cut ORFs, one of which (ORF1) coded for a 36.5 kDa polypeptide with conserved motifs of the '30K superfamily' movement proteins and the other (ORF2) encoded a 20 kDa polypeptide identified as the viral coat protein. RNA4, which was a little smaller than RNA3 (2078 nt versus 2438 nt), also differed from RNA3 in a few positions, but its in vitro translation did not produce any protein. By contrast, an additional RNA, 1042 nt in size with strong sequence homology with RNA3 and RNA4, was identified in RNA extracts from infected plants. This RNA, which may be a subgenomic form of RNA3 carrying the coat protein cistron, is apparently encapsidated to a very small extent, or not at all. Comparative computer-assisted analysis of virus-coded protein sequences disclosed homologies suggesting that OLV2 may belong to the family Bromoviridae, but as an entity separated from the currently known genera.

Detection of rice tungro bacilliform virus gene products in vivo

To study the products of the open reading frames (ORFs) of rice tungro bacilliform virus in rice plants the sequences containing ORFs I (encoding a 24-kDa protein, P24) and IV (P46) and the protease and polymerase (reverse transcriptase+RNaseH) domains of ORF III were cloned into a pGEX expression vector. The proteins, which were C-terminal fusions to glutathione S-transferase, were expressed in Escherichia coli and antisera were raised against them which, together with an antiserum against virus particles, was used to probe blots of proteins from infected and uninoculated plants and from virus preparations. The P24 antiserum detected virus-specific proteins of 74, 60, and 52 kDa, which are much bigger than expected. These proteins were found in virus preparations and immunogold labeling suggested that they might be internal in the particles. Virus-specific proteins of 33, 37, 62, and > 150 kDa were revealed by antiserum to virus particles. The antiserum to the protease revealed proteins of 13.5, 37, and 68 kDa both in extracts from infected plants and in purified virus preparations. This antiserum decorated intact virus particles as did the particle antiserum. The polymerase domain antiserum reacted with products of 56, 65, and 68 kDa in extracts from infected plants but not in virus particles. The antiserum to the ORF IV product did not detect any bands in either infected plant extracts or virus preparations. The significance of these products is discussed.

Nucleotide sequence of the 3' terminal region of the RNA of two filamentous grapevine viruses

The 3' terminal region of grapevine virus A (GVA) and grapevine virus B (GVB), encompassing 1883 and 2136 nucleotides, respectively, was sequenced by the deoxynucleotide chain termination method. Three putative open reading frames (ORF) were identified in both genomic viral RNAs, denoted 1 to 3 in the 5' to 3' direction. ORF 1 encoded a polypeptide with estimated M(r) of 31 kDa (GVA) and 36.5 kDa (GVB), possessing the G/D motif of the "30 K superfamily" movement proteins, and showing good alignments with putative movement proteins of trichoviruses and capilloviruses. ORF 2 was identified as the coat protein (CP) cistron, coding for polypeptides with an estimated M(r) of 21.5 kDa (GVA) and 21.6 kDa (GVB). These CPs showed substantial sequence homology with one another and with CPs of tricho- and capilloviruses, but not of closteroviruses. ORF 3 potentially coded for two small polypeptides with estimated M(r) of 10 kDa (GVA) and 14 kDa (GVB). The ORF 3 product of GVB (14 K), but not that of GVA, shared some homology with the 3' terminal polypeptides of different plant viruses that exhibit the "zinc finger domain" of proteins with nucleic acid-binding properties. GVA and GVB have many properties in common with trichoviruses but possess an extra open reading frame (ORF 3). Whether this finding may have a bearing on the classification of these viruses is unclear. However, until the taxonomic significance of this difference in genome structure is established, it seems plausible to include GVA and GVB as tentative species in the Trichovirus genus.

Sequence analysis of cymbidium ringspot virus satellite and defective interfering RNAs

The nucleotide sequences of cloned cDNA copies of satellite and defective interfering (DI) RNAs of cymbidium ringspot virus were determined. DI RNA is 499 nucleotides long and is composed of six stretches of sequence derived from CyRSV genomic RNA. Four of these stretches share common 5' sequences and the 5' and 3' ends are identical to those of genome RNA. Satellite RNA is 621 nucleotides long. In some regions the sequence is very similar (60% to 100% identical) to genomic RNA. A consensus sequence is proposed to be involved in the replication of genomic, DI and satellite RNAs.

Nucleotide sequence of the 3'-terminal region of cymbidium ringspot virus RNA

The nucleotide sequences of cDNA clones corresponding to 2569 nucleotides from the 3' end of cymbidium ringspot tombusvirus (CyRSV) RNA were determined. This region contains three open reading frames giving rise to three predicted protein products, two of which had been identified in previous studies. The 3' non-coding region is 351 nucleotides long. The amino acid sequence of CyRSV coat protein has striking similarities with that of tomato bushy stunt tombusvirus, particularly in the S domain. No homology was found between the protein encoded by the second largest open reading frame and the corresponding product of other plant viruses.