Phylogenetic analysis of viroid and viroid-like satellite RNAs from plants: a reassessment

The proposed monophyletic origin of a group of subviral plant pathogens (viroids and viroid-like satellite RNAs), as well as the phylogenetic relationships and the resulting taxonomy of these entities, has been recently questioned. The criticism comes from the (apparent) lack of sequence similarity among these RNAs necessary to reliably infer a phylogeny. Here we show that, despite their low overall sequence similarity, a sequence alignment manually adjusted to take into account all the local similarities and the insertions/deletions and duplications/rearrangements described in the literature for viroids and viroid-like satellite RNA, along with the use of an appropriate estimator of genetic distances, constitutes a data set suitable for a phylogenetic reconstruction. When the likelihood-mapping method was applied to this data set, the tree-likeness obtained was higher than that corresponding to a sequence alignment that does not take into consideration the local similarities. In addition, bootstrap analysis also supports the major groups previously proposed and the reconstruction is consistent with the biological properties of this RNAs.

Variations in diagnostic yield of head-up tilt test and electrophysiology in groups of patients with syncope of unknown origin

AIMS

To assess the diagnostic yield of the head-up tilt test and electrophysiology in different groups of patients with syncope of unknown origin established according to simple clinical criteria.

METHODS AND RESULTS

Six hundred consecutive patients with syncope of unknown origin submitted to a tilt test. Two hundred and forty seven of them also underwent electrophysiology. Patients were divided into groups according to age at the time of first syncope, ECG findings and the presence of organic heart disease. Positive responses to the tilt test were more common in patients who had suffered their first syncope at an age equal to or below 65 years (group I) than in older patients (group II) (47% vs 33%, P<0.05, OR 1.8, CI 1.2-2.78), and in patients with a normal ECG and without organic heart disease than in the other subgroups of patients (47% vs 37%, P<0.008, OR 1.6). The lowest rate of positive response was observed in older patients with an abnormal ECG and organic heart disease. Electrophysiology disclosed abnormal findings in group II more often than in group I (23% vs 7%, P<0.001, OR 3.7, CI 1.7-9.2). The diagnostic yield from electrophysiology was higher in patients with an abnormal ECG than in those with a normal ECG (22% vs 3.7%, P<0.0005, OR 7.1), and it was especially low in patients with a normal ECG and without organic heart disease (2.6%).

CONCLUSION

The diagnostic yield of the tilt test and electrophysiology differs in groups of patients with syncope of unknown origin, established according to simple clinical criteria. These findings have a bearing on selecting the most appropriate test in a particular patient.

Genetic diversity of Iberian populations of Bemisia tabaci (Hemiptera: Aleyrodidae) based on random amplified polymorphic DNA-polymerase chain reaction

The genetic structure of six Iberian populations of the whitefly Bemisia tabaci, two of them biotype Q, one biotype B, and the other three a mixture of both, has been studied using random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR). A total of 336 individuals was completely discriminated by means of 234 scored bands. Separate analyses of molecular variance of haploid males and diploid females using the pairwise number of differences between haplotypes showed that biotypes contribute significantly more to the observed variability than populations within biotypes. On average, gene flow between two biotypes of the same population is lower than between populations of identical biotypes. On the basis of these results and the nondetection under natural conditions of a single hybrid, we consider that both biotypes are genetically isolated under the ecological conditions prevailing in the south Iberian Peninsula. All populations of biotype Q presented similar values of intrapopulational diversity, which were higher than the values shown by populations of biotype B.

Famciclovir treatment in transplant recipients with HBV-related liver disease: disappointing results

OBJECTIVE

Long-term administration of hepatitis B immune globulin is effective as prophylaxis for hepatitis B virus (HBV) reinfection but is limited by cost, side effects, availability and a failure rate of 20%. Famciclovir has been shown to be effective in the treatment of hepatitis B in the immunocompetent patient. Fewer data exist in the liver transplant setting, particularly regarding its efficacy in de novo HBV infection. The aims of this pilot study were to determine the effectiveness and safety of long-term administration of famciclovir in recurrent (n = 3) and de novo (n = 3) HBV infection after liver transplantation.

METHODS

Six patients with postransplant HBV infection (positivity of serum HBsAg and HBV DNA), four of whom were HBeAg positive, were treated with famciclovir (500 mg, 3 times a day) with a minimum follow-up period of 12 months. Biochemical, serological, virological (HBV DNA by hybridization assays and polymerase chain reaction), and histological (including HBV immunostaining) endpoints were evaluated.

RESULTS

None of the patients had a complete biochemical response, with a near complete normalization of ALT levels being observed in 3/6 patients. There was a lack of correlation between virological and biochemical responses. None of the patients seroconverted to anti-HBs or anti-HBe. A virological clearance was observed in only two patients, whereas a moderate reduction in HBV DNA levels was present in one. HBV DNA levels were higher than levels during pretreatment in the three remaining patients. Histological improvement was only observed in one patient.

CONCLUSION

Famciclovir alone appears of limited efficacy in the treatment of HBV infection after liver transplantation.

Detecting changes in the functional constraints of paralogous genes

We describe a new procedure to determine whether regional alterations in the evolutionary constraints imposed on paralogous proteins have occurred. We used as models the A and B (alternatively called alpha and beta) subunits of V/F/A-ATPases, originated by a gene duplication more than 3 billion years ago. Changes associated to three major splits (eubacteria versus Archaea-eukaryotes; Archaea versus eukaryotes; and among free-living bacteria and symbiotic mitochondria) were studied. Only in the first case, when we compared eubacterial or mitochondrial F-ATPases versus eukaryotic vacuolar V-ATPases or archaeal A-ATPases, constraint changes were observed. Modifications in the degree of regional constraining were not detected for the other two types of comparisons (V-ATPases versus A-ATPases and within F-ATPases, respectively). When the rates of evolution of the two subunits were compared, it was found that F-ATPases regulatory subunits evolved faster than catalytic subunits, but the opposite was true for A- and V-ATPases. Our results suggest that, even for universal and essential proteins, selective constraints may be occasionally altered. On the other hand, in some cases no changes were detected after periods of more than 2.2 billion years.

Evidence for positive selection in the capsid protein-coding region of the foot-and-mouth disease virus (FMDV) subjected to experimental passage regimens

We present sequence data from two genomic regions of foot-and-mouth disease virus (FMDV) subjected to several experimental passage regimens. Maximum-likelihood estimates of the nonsynonymous-to-synonymous rate ratio parameter (d(N)/d(S)) suggested the action of positive selection on some antigenic sites of the FMDV capsid during some experimental passages. These antigenic sites showed an accumulation of convergent amino acid replacements during massive serial cytolytic passages and also in persistent infections of FMDV in cell culture. This accumulation was most significant at the antigenic site A (the G-H loop of capsid VP1), which includes an Arg-Gly-Asp (RGD) cellular recognition motif. Our analyses also identified a subregion of VP3, part of the fivefold axis of FMDV particles, that also appeared to be subjected to positive selection of amino acid replacements. From these results, we can conclude that under the restrictive conditions imposed either by the presence of the monoclonal antibodies, by the persistent infections, or by the competition processes established between different variants of the viral population, amino acid replacement in some capsid-coding regions can be positively selected toward an increase of those mutants with a higher capability to infect the cell.

Secretion pattern, ultrastructural localization and function of extracellular matrix molecules involved in eggshell formation

The chicken eggshell is a composite bioceramic containing organic and inorganic phases. The organic phase contains, among other constituents, type X collagen and proteoglycans (mammillan, a keratan sulfate proteoglycan, and ovoglycan, a dermatan sulfate proteoglycan), whose localization depends on a topographically defined and temporally regulated deposition. Although the distribution of these macromolecules in the eggshell has been well established, little is known about their precise localization within eggshell substructures and oviduct cells or their pattern of production and function during eggshell formation. By using immunofluorescent and immuno-ultrastructural analyses, we examined the distribution of these macromolecules in oviduct cells at different post-oviposition times. To understand the role of proteoglycan sulfation on eggshell formation, we studied the effects of inhibition of proteoglycan sulfation by treatment with sodium chlorate. We showed that these macromolecules are produced by particular oviduct cell populations and at precise post-oviposition times. Based on the precise ultrastructural localization of these macromolecules in eggshell substructures, the timing of the secretion of these macromolecules by oviduct cells and the effects on eggshell formation caused by the inhibition of proteoglycan sulfation, the putative role of mammillan is in the nucleation of the first calcite crystals, while that of ovoglycan is to regulate the growth and orientation of the later forming crystals of the chicken eggshell.

Shift- and scale-invariant recognition of contour objects with logarithmic radial harmonic filters

The phase-only logarithmic radial harmonic (LRH) filter has been shown to be suitable for scale-invariant block object recognition. However, an important set of objects is the collection of contour functions that results from a digital edge extraction of the original block objects. These contour functions have a constant width that is independent of the scale of the original object. Therefore, since the energy of the contour objects decreases more slowly with the scale factor than does the energy of the block objects, the phase-only LRH filter has difficulties in the recognition tasks when these contour objects are used. We propose a modified LRH filter that permits the realization of a shift- and scale-invariant optical recognition of contour objects. The modified LRH filter is a complex filter that compensates the energy variation resulting from the scaling of contour objects. Optical results validate the theory and show the utility of the newly proposed method.

Postsymbiotic plasmid acquisition and evolution of the repA1-replicon in Buchnera aphidicola

Buchnera aphidicola is an obligate, strictly vertically transmitted, bacterial symbiont of aphids. It supplies its host with essential amino acids, nutrients required by aphids but deficient in their diet of plant phloem sap. Several lineages of Buchnera show adaptation to their nutritional role in the form of plasmid-mediated amplification of key-genes involved in the biosynthesis of tryptophan (trpEG) and leucine (leuABCD). Phylogenetic analyses of these plasmid-encoded functions have thus far suggested the absence of horizontal plasmid exchange among lineages of Buchnera. Here, we describe three new Buchnera plasmids, obtained from species of the aphid host families Lachnidae and Pemphigidae. All three plasmids belong to the repA1 family of Buchnera plasmids, which is characterized by the presence of a repA1-replicon responsible for replication initiation. A comprehensive analysis of this family of plasmids unexpectedly revealed significantly incongruent phylogenies for different plasmid and chromosomally encoded loci. We infer from these incongruencies a case of horizontal plasmid transfer in Buchnera. This process may have been mediated by secondary endosymbionts, which occasionally undergo horizontal transmission in aphids.

Intravenous BQ-123 and phosphoramidon reduce ventricular ectopic beats and myocardial infarct size in dogs submitted to coronary occlusion and reperfusion

The aim of this work was to investigate the influence of endothelin on myocardial ischemia and reperfusion in anaesthetized dogs. Animals were submitted to left thoracotomy and 120 min of left anterior descending coronary occlusion, followed by 180 min of reperfusion. Arterial blood pressure and electrocardiogram (ECG) were recorded in order to analyze heart rate (HR)-pressure product and production of ectopic beats. Infarcted areas were identified by a macroscopic staining method and infarct size was expressed as percentage of risk zone. To inhibit the effects of endothelin in a group of animals, we administered intravenously an endothelin synthesis inhibitor (phosphoramidon) and in another group, an endothelin-1 A receptor blocker (BQ-123). Phosphoramidon decreased the HR-pressure product during reperfusion period, and both, phosphoramidon and BQ-123 decreased infarct size by 40% and the number of ventricular ectopic beats by 88% and 68%, respectively, as compared to the saline treated dogs. In conclusion, endothelin seems to play a deleterious role on the myocardium submitted to ischemia and reperfusion.

Dual-chamber pacing in the treatment of neurally mediated tilt-positive cardioinhibitory syncope : pacemaker versus no therapy: a multicenter randomized study. The Vasovagal Syncope International Study (VASIS) Investigators

BACKGROUND-This study was performed to compare implantation of a DDI pacemaker with rate hysteresis with no implant in respect to syncopal recurrences in patients with severe cardioinhibitory tilt-positive neurally mediated syncope. METHODS AND RESULTS-Forty-two patients from 18 European centers were randomized to receive a DDI pacemaker programmed to 80 bpm with hysteresis of 45 bpm (19 patients) or no pacemaker (23 patients). Inclusion criteria were >/=3 syncopes over the last 2 years and a positive cardioinhibitory (Vasovagal Syncope International Study types 2A and 2B) response to tilt testing. The median number of previous syncopal episodes was 6; asystolic response to tilt testing was present in 36 patients (86%) (mean asystole, 13.9+/-10.2 seconds). All patients were followed up for a minimum of 1.0 years and a maximum of 6.7 years (mean, 3.7+/-2.2). One patient (5%) in the pacemaker arm experienced recurrence of syncope compared with 14 patients (61%) in the no-pacemaker arm (P=0.0006). In the no-pacemaker arm, the median time to first syncopal recurrence was 5 months, with a rate of 0.44 per year. On repeated tilt testing performed within 15 days after enrollment, positive responses were observed in 59% of patients with pacemakers and in 61% of patients without pacemakers (P=NS). CONCLUSIONS-In a limited, select group of patients with tilt-positive cardioinhibitory syncope, DDI pacing with hysteresis reduced the likelihood of syncope. The benefit of the therapy was maintained over the long term. Even in untreated patients, the syncopal recurrence burden was low. A negative result of tilt testing was not a useful means to evaluate therapy efficacy.

The evolution of RNA viruses: A population genetics view

RNA viruses are excellent experimental models for studying evolution under the theoretical framework of population genetics. For a proper justification of this thesis we have introduced some properties of RNA viruses that are relevant for studying evolution. On the other hand, population genetics is a reductionistic theory of evolution. It does not consider or make simplistic assumptions on the transformation laws within and between genotypic and phenotypic spaces. However, such laws are minimized in the case of RNA viruses because the phenotypic space maps onto the genotypic space in a much more linear way than on higher DNA-based organisms. Under experimental conditions, we have tested the role of deleterious and beneficial mutations in the degree of adaptation of vesicular stomatitis virus (VSV), a nonsegmented virus of negative strand. We also have studied how effective population size, initial genetic variability in populations, and environmental heterogeneity shapes the impact of mutations in the evolution of vesicular stomatitis virus. Finally, in an integrative attempt, we discuss pros and cons of the quasispecies theory compared with classic population genetics models for haploid organisms to explain the evolution of RNA viruses.

Effect of deleterious mutation-accumulation on the fitness of RNA bacteriophage MS2

RNA viruses show the highest mutation rate in nature. It has been extensively demonstrated that, in the absence of purifying selection, RNA viruses accumulate deleterious mutations at a high rate. However, the parameters describing this accumulation are, in general, poorly understood. The present study reports evidences for fitness declines by the accumulation of deleterious mutations in the bacteriophage MS2. We estimated the rate of fitness decline to be as high as 16% per bottleneck transfer. In addition, our results agree with an additive model of fitness effects.

Effect of deleterious mutation-accumulation on the fitness of RNA bacteriophage MS2

RNA viruses show the highest mutation rate in nature. It has been extensively demonstrated that, in the absence of purifying selection, RNA viruses accumulate deleterious mutations at a high rate. However, the parameters describing this accumulation are, in general, poorly understood. The present study reports evidences for fitness declines by the accumulation of deleterious mutations in the bacteriophage MS2. We estimated the rate of fitness decline to be as high as 16% per bottleneck transfer. In addition, our results agree with an additive model of fitness effects.

Diminishing returns of population size in the rate of RNA virus adaptation

Whenever an asexual viral population evolves by adapting to new environmental conditions, beneficial mutations, the ultimate cause of adaptation, are randomly produced and then fixed in the population. The larger the population size and the higher the mutation rate, the more beneficial mutations can be produced per unit time. With the usually high mutation rate of RNA viruses and in a large enough population, several beneficial mutations could arise at the same time but in different genetic backgrounds, and if the virus is asexual, they will never be brought together through recombination. Thus, the best of these genotypes must outcompete each other on their way to fixation. This competition among beneficial mutations has the effect of slowing the overall rate of adaptation. This phenomenon is known as clonal interference. Clonal interference predicts a speed limit for adaptation as the population size increases. In the present report, by varying the size of evolving vesicular stomatitis virus populations, we found evidence clearly demonstrating this speed limit and thus indicating that clonal interference might be an important factor modulating the rate of adaptation to an in vitro cell system. Several evolutionary and epidemiological implications of the clonal interference model applied to RNA viruses are discussed.

The two faces of mutation: extinction and adaptation in RNA viruses

From a population standpoint, two main features characterize the replication of RNA viruses and viruses that use RNA as a replicative intermediate: high genetic variability, and enormous fluctuations in population size. Their genetic variability mainly reflects a lack of the proof-reading and post-replicative error correction mechanisms that operate during cellular DNA replication, but recombination and segment exchange can also play an important role. Viral population size can change tremendously as a consequence of transmission between hosts or between different tissues within an infected host. A new infection can be initiated with very few particles that subsequently expand many trillion-fold. Repeated bottleneck events can lead to drastic fitness losses or even to viral extinction, whereas continuously large population sizes result in fitness gains and adaptation. Here we review experimental evidence for the effects of mutation, selection, and genetic drift on the adaptation and extinction of RNA viruses.

The two faces of mutation: extinction and adaptation in RNA viruses

From a population standpoint, two main features characterize the replication of RNA viruses and viruses that use RNA as a replicative intermediate: high genetic variability, and enormous fluctuations in population size. Their genetic variability mainly reflects a lack of the proof-reading and post-replicative error correction mechanisms that operate during cellular DNA replication, but recombination and segment exchange can also play an important role. Viral population size can change tremendously as a consequence of transmission between hosts or between different tissues within an infected host. A new infection can be initiated with very few particles that subsequently expand many trillion-fold. Repeated bottleneck events can lead to drastic fitness losses or even to viral extinction, whereas continuously large population sizes result in fitness gains and adaptation. Here we review experimental evidence for the effects of mutation, selection, and genetic drift on the adaptation and extinction of RNA viruses.

Flow cytometric analysis of peroxidative activity in granulocytes from coronary and peripheral blood in acute myocardial ischemia and reperfusion in dogs: protective effect of methionine

BACKGROUND

Methionine has shown protective effects in experimental models of myocardial infarction and is highly reactive to oxidative compounds produced by polymorphonuclear leukocytes (PMN), which in turn have been associated with myocardial damage. We have investigated the effect of methionine administration on spontaneous leukocyte peroxidative activity in myocardial ischemia and reperfusion.

METHODS

In anesthetized dogs, with coronary occlusion (90 min) and reperfusion (90 min), PMN activation was measured by flow cytometric determination of H(2)O(2) with dihydrorhodamine 123, and correlated to hemodynamic parameters and infarct presence. To assess a possible direct effect of methionine, H(2)O(2) and superoxide were measured by flow cytometry in dog leukocyte suspensions following in vitro stimulation with f-MLP.

RESULTS

PMN peroxidative activity in saline-treated dogs increased significantly after coronary occlusion and after reperfusion. These changes were greater in coronary venous blood than in femoral blood. Methionine administration (150 mg/kg, i.v.) before occlusion totally suppressed PMN activation, both after occlusion and reperfusion.

CONCLUSIONS

PMN are promptly activated in myocardial ischemia, and methionine administration prevents such activation. However, methionine has no direct effect on spontaneous peroxidative activity, and f-MLP induced peroxidative activity. These in vivo effects of methionine, may additionally contribute to explain its protective role in experimental -788-877-7QQ8-8-7-88-8-8778--8Q78-----8--8-Q-7-Q7----- --------------8888 888888-7777777777777777777777777777777----------------888888888888888888 8877777--87--------8-----------------7-8888-887-----------8----8-8-87777 7777777------------------------------------------------------T7OW

Apo E influences declarative and procedural learning in age-associated memory impairment

Age-associated memory impairment (AAMI) is a clinical entity which was originally described to define memory problems linked to normal aging. Apolipoprotein E and ACE genes have both been associated with cognitive impairment in aging and dementia. The purpose of this study was to investigate memory and executive functions in AAMI according to the genetic background. We found that subjects carrying the Apo E epsilon4 allele exhibit lower memory performance on tests of both declarative and procedural memory. We did not find differences on frontal lobe tests. These findings give further support to the hypothesis concerning a genetic susceptibility for cognitive impairment in aging.

Clonal interference and the evolution of RNA viruses

In asexual populations, beneficial mutations that occur in different lineages compete with one another. This phenomenon, known as clonal interference, ensures that those beneficial mutations that do achieve fixation are of large effect. Clonal interference also increases the time between fixations, thereby slowing the adaptation of asexual populations. The effects of clonal interference were measured in the asexual RNA virus vesicular stomatitis virus; rates and average effects of beneficial mutations were quantified.

The genetic structure of Drosophila subobscura populations from the Islands of Majorca and Minorca (Balearic Islands, Spain) based on allozymes and mitochondrial DNA

The genetic structure of seven populations of Drosophila subobscura from different locations on Majorca and Minorca (Balearic Islands, Spain) was studied using two types of markers: allozyme and mitochondrial DNA restriction analyses. Both markers showed congruent results. In the allozyme data, when the Acph-1 locus was excluded from the joint FST statistics, only three out of 21 comparisons were statistically significant, lending support to the hypothesis of low genetic differentiation. The mtDNA restriction analyses showed two haplotypes at a high frequency (more than 40% each), irrespective of the location considered, and a number of endemic haplotypes at very low frequencies (not higher than 2% each). The analyses of the genetic structure yielded a pattern similar to the allozymes. The cytonuclear disequilibrium analyses showed the difficulty of detecting cytonuclear associations in natural populations because they are mainly transient.

Genetic differentiation in the striped dolphin Stenella coeruleoalba from European waters according to mitochondrial DNA (mtDNA) restriction analysis

We used mitochondrial DNA (mtDNA) restriction analysis to study genetic variation in 98 striped dolphins (Stenella coeruleoalba) stranded on coasts from different European countries and from animals caught by fisheries. A total of 63 different restriction sites was mapped after digestion of mtDNA with 15 restriction endonucleases that yielded a total of 27 haplotypes. No haplotype was shared between Mediterranean and Atlantic areas. All the analyses indicate the existence of two different populations with a very limited gene flow across the Strait of Gibraltar.

Effect of etilefrine in preventing syncopal recurrence in patients with vasovagal syncope: a double-blind, randomized, placebo-controlled trial. The Vasovagal Syncope International Study

BACKGROUND

Etilefrine is an alpha-agonist agent with a potent vasoconstrictor effect, which is potentially useful in preventing vasovagal syncope by reducing venous pooling and/or by counteracting reflex arteriolar vasodilatation. The present multicenter, randomized, placebo-controlled study was designed to evaluate the efficacy of this drug for the long-term management of patients with recurrent vasovagal syncope.

METHODS AND RESULTS

In the 20 participating centers, 126 patients with recurrent vasovagal syncope (at least 3 episodes in the last 2 years) and a positive baseline head-up tilt response were randomly assigned to placebo (63 patients) or etilefrine at a dosage of 75 mg/d (63 patients) and were followed up for 1 year or until syncope recurred. The primary end-point of the study was the first recurrence of syncope. There were no differences between the 2 study groups in the patients' baseline characteristics. During follow-up, the group treated with etilefrine had a similar incidence of first syncopal recurrence to that of placebo group both in the intention-to-treat analysis (24% versus 24%) and in on- treatment analysis (26% versus 24%). Moreover, the median time to the first syncopal recurrence did not significantly differ between the 2 study groups (106 days in the etilefrine arm and 112 days in the placebo arm).

CONCLUSIONS

Oral etilefrine is not superior to placebo in preventing spontaneous episodes of vasovagal syncope. Randomized controlled studies are essential to assess the real usefulness of any proposed therapy for patients with vasovagal syncope.