RNAcentral: A vision for an international database of RNA sequences

During the last decade there has been a great increase in the number of noncoding RNA genes identified, including new classes such as microRNAs and piRNAs. There is also a large growth in the amount of experimental characterization of these RNA components. Despite this growth in information, it is still difficult for researchers to access RNA data, because key data resources for noncoding RNAs have not yet been created. The most pressing omission is the lack of a comprehensive RNA sequence database, much like UniProt, which provides a comprehensive set of protein knowledge. In this article we propose the creation of a new open public resource that we term RNAcentral, which will contain a comprehensive collection of RNA sequences and fill an important gap in the provision of biomedical databases. We envision RNA researchers from all over the world joining a federated RNAcentral network, contributing specialized knowledge and databases. RNAcentral would centralize key data that are currently held across a variety of databases, allowing researchers instant access to a single, unified resource. This resource would facilitate the next generation of RNA research and help drive further discoveries, including those that improve food production and human and animal health. We encourage additional RNA database resources and research groups to join this effort. We aim to obtain international network funding to further this endeavor.     

Characterization of the genetic diversity of <Emphasis Type="Italic">Mycobacterium tuberculosis</Emphasis> in São Paulo city,Brazil

Background

Tuberculosis is a major health problem in São Paulo, Brazil, which is the most populous and one of the most cosmopolitan cities in South America. To characterize the genetic diversity of Mycobacterium tuberculosis in the population of this city, the genotyping techniques of spoligotyping and MIRU were applied to 93 isolates collected in two consecutive years from 93 different tuberculosis patients residing in São Paulo city and attending the Clemente Ferreira Institute (the reference clinic for the treatment of tuberculosis).

Findings

Spoligotyping generated 53 different spoligotype patterns. Fifty-one isolates (54.8%) were grouped into 13 spoligotyping clusters. Seventy- two strains (77.4%) showed spoligotypes described in the international databases (SpolDB4, SITVIT), and 21 (22.6%) showed unidentified patterns. The most frequent spoligotype families were Latin American Mediterranean (LAM) (26 isolates), followed by the T family (24 isolates) and Haarlem (H) (11 isolates), which together accounted for 65.4% of all the isolates. These three families represent the major genotypes found in Africa, Central America, South America and Europe. Six Spoligo-International-types (designated SITs by the database) comprised 51.8% (37/72) of all the identified spoligotypes (SIT53, SIT50, SIT42, SIT60, SIT17 and SIT1). Other SITs found in this study indicated the great genetic diversity of M. tuberculosis, reflecting the remarkable ethnic diversity of São Paulo city inhabitants. The MIRU technique was more discriminatory and did not identify any genetic clusters with 100% similarity among the 93 isolates. The allelic analysis showed that MIRU loci 26, 40, 23 and 10 were the most discriminatory. When MIRU and spoligotyping techniques were combined, all isolates grouped in the 13 spoligotyping clusters were separated.

Conclusions

Our data indicated the genomic stability of over 50% of spoligotypes identified in São Paulo and the great genetic diversity of M. tuberculosis isolates in the remaining SITs, reflecting the large ethnic mix of the São Paulo city inhabitants. The results also indicated that in this city, M. tuberculosis isolates acquired drug resistance independently of genotype and that resistance was more dependent on the selective pressure of treatment failure and the environmental circumstances of patients.

     

Biogeographical analysis of two Polypodium species complexes (Polypodiaceae) in Mexico and Central America

We analyzed the geographical and elevational distributions of two Polypodium complexes from Mexico and Central America. Distribution data of nine species of the Polypodium colpodes complex and the Polypodium plesiosorum complex were obtained from almost 1500 herbarium specimens, field collections in Mexico and Costa Rica, and literature studies. The presence of each species was recorded for each Mesoamerican country, in 1° × 1° grid‐cells and biogeographical provinces. The rarity of species was also evaluated. Although the two complexes show extensive overlap, the P. colpodes complex is distributed mainly along the Pacific versant of Mexico and Central America, whereas the P. plesiosorum complex occurs mainly along the Atlantic versant. Those biogeographical provinces with maximum species diversity are Chiapas (seven species), Sierra Madre del Sur (six species), and the Trans‐Mexican Volcanic belt (six species). Grid‐cells with more species are located mainly in the mountains of central‐southern Mexico and northern Central America. Richness does not decrease or increase with latitude. Elevation distributions showed that most Polypodium species are concentrated in the montane interval and three species groups were recognized based on elevational preferences. Polypodium colpodes and P. plesiosorum are the most widely distributed species, whereas Polypodium castaneum and Polypodium flagellare are the only two species that possess the three attributes of rarity (narrow geographical distribution, high habitat specificity, and scarce local populations). Polypodium species of both complexes are present mainly in the montane regions of the study area and show some degree of geographical sympatry, especially in southern Mexico and northern Central America. This overlapping is explained by the elevation tolerance within montane systems and because most species inhabit three or more vegetation types. The distributional patterns of these complexes coincided with the three regional highlands of Mesoamerica, which are separated from each other by the Isthmus of Tehuantepec and by the lowlands of Nicaragua. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

Role of plant functional traits in determining vegetation composition of abandoned grazing land in north‐eastern Victoria,Australia

Question: In the Northern Hemisphere, species with dispersal limitations are typically absent from secondary forests. In Australia, little is known about dispersal mechanisms and other traits that drive species composition within post‐agricultural, secondary forest. We asked whether mode of seed dispersal, nutrient uptake strategy, fire response, and life form in extant vegetation differ according to land‐use history. We also asked whether functional traits of Australian species that confer tolerance to grazing and re‐colonisation potential differ from those in the Northern Hemisphere. Location: Delatite Peninsula, NE Victoria, Australia. Methods: The vegetation of primary and secondary forests was surveyed using a paired‐plot design. Eight traits were measured for all species recorded. ANOSIM tests and Non‐metric Multi‐dimensional Scaling were used to test differences in the abundance of plant attributes between land‐use types. Results: Land‐use history had a significant effect on vegetation composition. Specific leaf area (SLA) proved to be the best predictor of response to land‐use change. Primary forest species were typically myrmecochorous phanerophytes with low SLA. In the secondary forest, species were typically therophytes with epizoochorous dispersal and high SLA. Conclusions: The attributes of species in secondary forests provide tolerance to grazing suggesting that disturbance caused by past grazing activity determined the composition of these forests. Myrmecochores were rare in secondary forests, suggesting that species had failed to re‐colonise due to dispersal limitations. Functional traits that resulted in species loss through disturbance and prevented re‐colonisation were different to those in the Northern Hemisphere and were attributable to the sclerophyllous nature of the primary forest.     

Inhibition of Müller glial cell division blocks regeneration of the light-damaged zebrafish retina

The adult zebrafish retina possesses a robust regenerative response. In the light-damaged retina, Müller glial cell divisions precede regeneration of rod and cone photoreceptors. Neuronal progenitors, which arise from the Müller glia, continue to divide and use the Müller glial cell processes to migrate to the outer nuclear layer and replace the lost photoreceptors. We tested the necessity of Müller glial cell division for photoreceptor regeneration. As knockdown tools were unavailable for use in the adult zebrafish retina, we developed a method to conditionally inhibit the expression of specific proteins by in vivo electroporation of morpholinos. We determined that two separate morpholinos targeted against the proliferating cell nuclear antigen (PCNA) mRNA reduced PCNA protein levels. Furthermore, injection and in vivo electroporation of PCNA morpholinos immediately prior to starting intense light exposure inhibited both Müller glial cell proliferation and neuronal progenitor marker Pax6 expression. PCNA knockdown additionally resulted in decreased expression of glutamine synthetase in Müller glia and Müller glial cell death, while amacrine and ganglion cells were unaffected. Finally, histological and immunological methods showed that long-term effects of PCNA knockdown resulted in decreased numbers of Müller glia and the failure to regenerate rod photoreceptors, short single cones, and long single cones. These data suggest that Müller glial cell division is necessary for proper photoreceptor regeneration in the light-damaged zebrafish retina and are consistent with the Müller glia serving as the source of neuronal progenitor cells in regenerating teleost retinas.     

Effects of smoke,heat and charred wood on the germination of dormant soil‐stored seeds from a Eucalyptus baxteri heathy‐woodland in Victoria,SE Australia

The effects of dry heat, wet heat, charred wood and smoke on the germination of dormant soil‐stored seeds from a Eucalyptus woodland in western Victoria were tested by using a glasshouse seed‐bank germination experiment. Seedling density, species richness and species composition were compared between replicated treated and control samples. A total of 5922 seedlings, comprising 59 plant species, was recorded from the soil samples over a period of 150 days. While a few species dominated (including Centrolepis strigosa, Wahlenbergia gracilenta and Ixodia achillaeoides), 26 species were represented by fewer than five seedlings and 18 species were restricted to single treatment types. With the exception of charred wood, all treatments led to a significant increase in seed germination relative to the control. The highest number of germinants was obtained for the smoke treatment, with a mean (± SE) of 12 547 ± 449 seedlings m^–2. Heat treatments yielded intermediate densities, with means (± SE) varying between 7445 ± 234 and 9133 ± 445 seedlings m^–2. In comparison with the estimates of seed‐bank sizes from other fire‐prone ecosystems, these densities are high. Species richness differed significantly among treatments. Highest mean richness was recorded in the smoke treatment and lowest for the control and charred wood treatments. There were significant differences in seed‐bank species composition between treatment types based on analysis of similarity (Anosim) using Bray–Curtis similarity. While heat was a specific requirement for triggering germination in hard‐seeded species (e.g. Fabaceae), smoke was the most effective trigger for species from a broad range of other families. The potentially confounding effect of physical and chemical mechanisms of germination stimulation in heated bulk soil samples is raised as an issue requiring further investigation in relation to the role of smoke as a germination trigger.