Small sample sizes in high-throughput miRNA screens: A common pitfall for the identification of miRNA biomarkers

Since the discovery of microRNAs (miRNAs), circulating miRNAs have been proposed as biomarkers for disease. Consequently, many groups have tried to identify circulating miRNA biomarkers for various types of diseases including cardiovascular disease and cancer. However, the replicability of these experiments has been disappointingly low. In order to identify circulating miRNA candidate biomarkers, in general, first an unbiased high-throughput screen is performed in which a large number of miRNAs is detected and quantified in the circulation. Because these are costly experiments, many of such studies have been performed using a low number of study subjects (small sample size). Due to lack of power in small sample size experiments, true effects are often missed and many of the detected effects are wrong. Therefore, it is important to have a good estimate of the appropriate sample size for a miRNA high-throughput screen. In this review, we discuss the effects of small sample sizes in high-throughput screens for circulating miRNAs. Using data from a miRNA high-throughput experiment on isolated monocytes, we illustrate that the implementation of power calculations in a high-throughput miRNA discovery experiment will avoid unnecessarily large and expensive experiments, while still having enough power to be able to detect clinically important differences. Keywords: MicroRNA, High-throughput screens, Biomarkers, Small sample size error, Array, Methodolog

Micro-analytical and molecular approaches for understanding the distribution, biochemistry, and molecular biology of selenium in (hyperaccumulator) plants

Selenium (Se) is not essential for plants and is toxic at high concentrations. However, Se hyperaccumulator plants have evolved strategies to both tolerate and accumulate>1000 µg Se g−1 DW in their living above-ground tissues. Given the complexity of the biochemistry of Se, various approaches have been adopted to study Se metabolism in plants. These include X-ray-based techniques for assessing distribution and chemical speciation of Se, and molecular biology techniques to identify genes implicated in Se uptake, transport, and assimilation. This review presents these techniques, synthesises the current state of knowledge on Se metabolism in plants, and highlights future directions for research into Se (hyper)accumulation and tolerance. We conclude that powerful insights may be gained from coupling information on the distribution and chemical speciation of Se to genome-scale studies to identify gene functions and molecular mechanisms that underpin Se tolerance and accumulation in these ecologically and biotechnologically important plants species. The study of Se metabolism is challenging and is a useful testbed for developing novel analytical approaches that are potentially more widely applicable to the study of the regulation of a wide range of metal(loid)s in hyperaccumulator plants.Katherine Pinto Irish, Maggie, Anne Harvey, Hugh H. Harris, Mark G. M. Aarts, Cheong Xin Chan, Peter D. Erskine, Antony van der En

Abundance, habitat use and diet of Callicebus nigrifrons Spix (Primates, Pitheciidae) in Cantareira State Park, São Paulo, Brazil Abundância, uso do habitat e dieta de Callicebus nigrifrons É. Geoffroy (Primates, Pitheciidae) no Parque Estadual da Cantareira, São Paulo, Brasil

Between april 2005 and May 2006, according to the pressuposts of line transect methodology, census were carried to estimate abundance and population density of Callicebus nigrifrons Spix, 1823 (Pitheciidae) in Cantareira State Park, State of São Paulo, southeastern Brazil (23&deg;23'42"S, 46&deg;35'27"W). After 275.80 Km of census sampling effort, the titis were the second most abundant primate species, presenting an abundance index of 1.4 groups for each 10 km walked and a density estimate of 12.21 ind./km² (ranging between 8.45 a 17.63 ind./km²). The collection of ancillary data during the census allowed the determination of diet and habitat use by the titis groups, and results show a relative adaptability to disturbed habitats.<br>Entre abril de 2005 e maio de 2006, através de censos seguindo os pressupostos da metodologia de transecção linear, foram estimadas a densidade populacional e abundância de Callicebus nigrifrons Spix, 1823 (Pitheciidae) no Parque Estadual da Cantareira, Estado de São Paulo, Sudeste do Brasil (23&deg;23'42"S, 46&deg;35'27"W). Com um esforço amostral de 275,8 km de censos, os sauás foram a segunda espécie de primata mais abundante, apresentando um índice de abundância de 1,4 grupos para cada 10 km percorridos e uma estimativa de densidade de 12,21 ind./km² (variando de 8,45 a 17,63 ind./km²). A coleta de dados auxiliares durante os censos possibilitou a verificação da dieta e uso do hábitat pelos grupos de Callicebus, e os resultados evidenciaram uma relativa adaptabilidade à ambientes perturbados

Padrões de floração e frutificação de árvores da Amazônia Maranhense Flowering and Fruiting Patterns of the Maranhense Amazon Rainforest Trees

Estudos fenológicos em nível de comunidades podem facilitar a compreensão do comportamento das espécies diante de alterações nos ecossistemas, além de refletir a distribuição anual de tipos específicos de recursos. Este trabalho buscou definir os padrões gerais e a sazonalidade de floração e frutificação de uma comunidade em duas áreas de floresta na Amazônia Maranhense, uma não perturbada e outra submetida a corte seletivo. A vegetação corresponde às matas de cipós das florestas amazônicas, alternando matas densas e abertas, de alta biomassa. Valores médios anuais de temperatura variam entre 24,5º C e 26,0º C, e entre 1400 mm e 1800 mm de precipitação, com um período seco de 5 a 6 meses, de junho a novembro. Foram analisadas a floração e a frutificação de 89 espécies arbóreas, de agosto de 1994 a junho de 1996. As espécies foram agrupadas em: árvores do sub-dossel, árvores do estrato superior e árvores que ocorrem em ambos os estratos. Foi feita comparação entre grupos (estratos, tipos de floresta e mecanismos de dispersão) e possíveis correlações com a precipitação foram investigadas. Quinze espécies estudadas foram exclusivas do estrato inferior e 63 do estrato superior da floresta; 17 espécies foram registradas apenas na mata nativa e 37 apenas na mata manejada. A maioria das espécies é zoocórica (62,9 %). A floração e a frutificação ocorreram durante todo o ano, com pico de floração de outubro a dezembro e picos de frutificação de março a julho e de outubro a dezembro. Os resultados obtidos demonstram uma grande sincronia na floração e frutificação dos indivíduos, e confirmam a relação entre esses processos e a variação na precipitação ao longo do ano, e que plantas de ambientes diferenciados exibem comportamentos fenológicos diferentes. Os padrões observados foram semelhantes entre as áreas e a outros estudos na Amazônia.<br>Community level phonological studies can facilitate the understanding of species behavior as a result of ecosystem changes, further reflecting on the annual allotment of specific resources. The aim of the present study was to define the general patterns, flowering and fruiting seasonality from a community in two forest areas of the Maranhense Amazon Rainforest: a non-disturbed area and another submitted to selective logging. The vegetation is composed of Amazon forest lianas alternating between dense and open high biomass forest. Average annual temperature varies between 24.5O C and 26.0O C, with precipitation ranging from 1400 mm to 1800 mm, and a dry season between June and November. Flowering and fruiting of 89 species were analyzed from August 1994 to June 1996. The species were grouped as follows: sub-dossal, upper strata, and trees occurring in both strata. Comparison was made between groups (strata, types of forest and mechanisms for dispersal) and possible correlations with rainfall were investigated. Fifteen studied species were solely from the lower strata, and 63 from the upper forest strata; 17 species were recorded only in native forest and 37 in managed forest. Most species (62.9 %) is zoochorous. Flowering and fruiting take place throughout the year with flowering peak from October to December and fruiting peaks from March to July and from October to December. The results showed a great synchrony in flowering and fruiting of individuals, and confirm the relationship between these cases and the variation in rainfall throughout the year, and that plants of different environments exhibit phonological behavior different. The observed flowering and fruiting patterns were similar between the areas and comparable to other studies in the Amazon Rainforest