An RNA folding method capable of identifying pseudoknots and base triples

MOTIVATION: Recently, we described a Maximum Weighted Matching (MWM) method for RNA structure prediction. The MWM method is capable of detecting pseudoknots and other tertiary base-pairing interactions in a computationally efficient manner (Cary and Stormo, Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology, pp. 75-80, 1995). Here we report on the results of our efforts to improve the MWM method's predictive accuracy, and show how the method can be extended to detect base interactions formerly inaccessible to automated RNA modeling techniques. RESULTS: Improved performance in MWM structure prediction was achieved in two ways. First, new ways of calculating base pair likelihoods have been developed. These allow experimental data and combined statistical and thermodynamic information to be used by the program. Second, accuracy was improved by developing techniques for filtering out spurious base pairs predicted by the MWM program. We also demonstrate here a means by which the MWM folding method may be used to detect the presence of base triples in RNAs. AVAILABILITY: http://www.cshl.org/mzhanglab/tabaska/j axpage. html CONTACT: tabaska@cshl.org      

The evolutionary history of Drosophila buzzatii. XXX. Mitochondrial DNA polymorphism in original and colonizing populations

Both original and colonizer populations of Drosophila buzzatii have been analyzed for mtDNA restriction polymorphisms. Most of the mtDNA nucleotide variation in original populations of NW Argentina can be explained by intrapopulation diversity and only a small fraction can be accounted for by between-population diversity. Similar results are obtained using either the estimated number of nucleotide substitutions per site or considering each restriction site as a locus. Colonizer populations of the Iberian Peninsula are monomorphic and show only the most common haplotype from the original populations. Under the infinite island model and assuming that populations are in equilibrium, fixation indices indicate enough gene flow to explain why the populations are not structured. Yet, the possibility exists that populations have not reached an equilibrium after a founder event at the end of the last Pleistocene glaciation. Tajima's test suggests that directional selection and/or a recent bottleneck could explain the present mtDNA differentiation. Considering the significant population structure found for the chromosomal and some allozyme polymorphisms, the among- population uniformity for mtDNA variability argues in favor of the chromosomal and some allozyme polymorphisms being adaptive.      

Immunological similarities between specific chloroplast ribosomal proteins from Chlamydomonas reinhardtii and ribosomal proteins from Escherichia coli

Polyclonal antibodies were elicited against seven of the 33 different proteins of the large subunit of the chloroplast ribosome from Chlamydomonas reinhardtii. Three of these proteins are synthesized in the chloroplast and four are made in the cytoplasm and imported. In western blots, six of the seven antisera are monospecific for their respective large subunit ribosomal proteins, and none of these antisera cross-reacted with any chloroplast small subunit proteins from C. reinhardtii. Antisera to the three chloroplast-synthesized ribosomal proteins cross-reacted with specific Escherichia coli large subunit proteins of comparable charge and molecular weight. Only one of the four antisera to the chloroplast ribosomal proteins synthesized in the cytoplasm cross-reacted with an E. coli large subunit protein. None of the antisera cross-reacted with any E. coli small subunit proteins. On the assumption of a procaryotic, endosymbiotic origin for the chloroplast, those chloroplast ribosomal proteins still synthesized within the organelle appear to have retained more antigenic sites in common with E. coli ribosomal proteins than have those which are now the products of cytoplasmic protein synthesis. Antisera to this cytoplasmically synthesized group of chloroplast ribosomal proteins did not recognize any antigenic sites among C. reinhardtii cytoplasmic ribosomal proteins, suggesting that the genes for the cytoplasmically synthesized chloroplast ribosomal proteins either are not derived from the cytoplasmic ribosomal protein genes or have evolved to a point where no antigenic similarities remain.      

Life-history trade-off in two predator species sharing the same prey: a study on cassava-inhabiting mites

In cassava fields, two species of predatory mites, Typhlodromalus aripo and T. manihoti, co-occur at the plant level and feed on Mononychellus tanajoa , a herbivorous mite. The two predator species are spatially segregated within the plant: T. manihoti dwells on the middle leaves, while T. aripo occurs in the apices of the plant during the day and moves to the first leaves below the apex at night.
To monitor the prey densities experienced by the two predator species in their micro-environment, we assessed prey and predator populations in apices and on the leaves of cassava plants in the field. Prey densities peaked from November to January and reached the lowest levels in July. They were higher on leaves than in the apices. To test whether the life histories of the two predator species are tuned to the prey density they experience, we measured age-specific fecundity and survival of the two predators under three prey density regimes (1 prey female/72 h, 1 prey female/24 h and above the predators level of satiation). T. manihoti had a higher growth rate than T. aripo at high prey densities, mainly due to its higher fecundity. T. aripo had a higher growth rate at low prey density regimes, due to its late fecundity and survival. Thus, each of the two species perform better under the prey density that characterizes their micro-habitat within the plant.     

Nine months in space: effects on human autonomic cardiovascular regulation.

We studied three Russian cosmonauts to better understand how long-term exposure to microgravity affects autonomic cardiovascular control. We recorded the electrocardiogram, finger photoplethysmographic pressure, and respiratory flow before, during, and after two 9-mo missions to the Russian space station Mir. Measurements were made during four modes of breathing: 1) uncontrolled spontaneous breathing; 2) stepwise breathing at six different frequencies; 3) fixed-frequency breathing; and 4) random-frequency breathing. R wave-to-R wave (R-R) interval standard deviations decreased in all and respiratory frequency R-R interval spectral power decreased in two cosmonauts in space. Two weeks after the cosmonauts returned to Earth, R-R interval spectral power was decreased, and systolic pressure spectral power was increased in all. The transfer function between systolic pressures and R-R intervals was reduced in-flight, was reduced further the day after landing, and had not returned to preflight levels by 14 days after landing. Our results suggest that long-duration spaceflight reduces vagal-cardiac nerve traffic and decreases vagal baroreflex gain and that these changes may persist as long as 2 wk after return to Earth.     

Exploring the genetics of aging in a wild passerine bird

Senescence is the decline in survival and reproduction as an organism ages and is known to occur in collared flycatchers Ficedula albicollis. We consider annual fitness (the estimated genetic contribution that an individual makes to next year's gene pool) as a measure of age-specific fitness. We apply a restricted maximum likelihood linear mixed-model approach on 25 years of data on 3,844 male and 4,992 female collared flycatchers. Annual fitness had a significant additive genetic component (h2 of about 4%). Annual fitness declined at later ages in both sexes. Using a random regression animal model, we show that the observed age-related phenotypic changes in annual fitness were not present on the additive genetic level, contrary to predictions of genetic hypotheses of senescence. Our study suggests that patterns of aging in the wild need to be interpreted with caution in terms of underlying genetics because they may be largely determined by environmental processes.     

Influence of Habitat Quality and Patch Size on Occupancy and Persistence in two Populations of the Apollo Butterfly (Parnassius apollo)

Recent studies on butterflies emphasize habitat characteristics together with metapopulation parameters (patch area and isolation) giving a more thorough understanding of processes influencing population persistence and patch occupancy, than either of them alone. We studied a coastal and an archipelago population of the Apollo butterfly (Parnassius apollo) in SW Finland. Larvae were surveyed for four years in both populations. Counting larvae on three consecutive days and temporarily removing them tested the survey accuracy. The removals showed four times higher larval abundance in the archipelago than on the coast. Survey methods were reliable, provided that empty patch status was not based on single visits only, if larval abundance was low. On the coast, large patches, and patches with high host-plant abundance were often occupied. In the archipelago, patches rich in host-plant were often occupied whereas patch area did not affect patch occupancy. In both populations, the probability of patches being occupied for three consecutive years increased with increasing host-plant abundance and patch area. Conservation of P. apollo depends on securing host-plant abundance on large enough patches in both study systems. In these systems, even crude habitat measures prove useful for understanding ecological processes behind observed patterns.