We analyzed gene expression in marine and freshwater bacterioplankton communities by the direct retrieval and analysis of microbial transcripts. Environmental mRNA, obtained from total RNA by subtractive hybridization of rRNA, was reverse transcribed, amplified with random primers, and cloned. Approximately 400 clones were analyzed, of which ϳ80% were unambiguously mRNA derived. mRNAs appeared to be from diverse taxonomic groups, including both Bacteria (mainly ␣-and ␥-Proteobacteria) and Archaea (mainly Euryarchaeota). Many transcripts could be linked to environmentally important processes such as sulfur oxidation (soxA), assimilation of C1 compounds (fdh1B), and acquisition of nitrogen via polyamine degradation (aphA). Environmental transcriptomics is a means of exploring functional gene expression within natural microbial communities without bias toward known sequences, and provides a new approach for obtaining communityspecific variants of key functional genes.
Abstract. The importance of lianas through time and their effect on tree reproduction are evaluated for the first time in a Southeast Asian Dipterocarp forest. We quantified flower and seed production by lianas and trees for 13 years, assessed liana loads in the crowns of all trees larger than 30 cm in diameter at breast height (1.3 m) in 2002 and 2014, and assessed levels of reproduction for the same trees during a strong general flowering event in 2014 for the 50-ha forest dynamics plot at the Pasoh Forest Reserve, Malaysia. General flowering refers to synchronous reproduction by hundreds of plant species at irregular, multiyear intervals and only occurs in Southeast Asian Dipterocarp forests. Overall, lianas were present in 50% of tree crowns and comprised 31% of flower production and 46% of seed production. Lianas reduced growth, survival, and reproduction by their host trees. Lianas were less frequent in canopyemergent trees, Dipterocarps comprised a disproportionately large proportion of canopy emergents, and, as a consequence, lianas were less frequent in Dipterocarps than in trees from other plant families. Lianas infested the crowns of significantly fewer trees in 2014 (47.9%) than in 2002 (52.3%); however, the decrease was restricted to trees with the lightest liana loads and sample sizes and statistical power were enormous. Lianas comprised a stable proportion of flower production and a highly variable proportion of seed production from 2002 through 2013. We conclude lianas have a huge impact on trees in this forest and were a stable component of the forest between 2002 and 2014. The emergent habit and associated ability to avoid lianas might contribute to the success of the Dipterocarpaceae.
The small round blue cell tumors of childhood, which include neuroblastoma, rhabdomyosarcoma, nonHodgkin's lymphoma, and the Ewing's family of tumors, are so called because of their similar appearance on routine histology. Using cDNA microarray gene expression profiles and artificial neural networks (ANNs), we previously identified 93 genes capable of diagnosing these cancers. Using a subset of these, together with some additional genes (total 39), we developed a multiplex polymerase chain reaction (PCR) assay to diagnose these cancer types. Blinded testing of 96 new samples (26 Ewing's family of tumors, 29 rhabdomyosarcomas, 24 neuroblastomas, and 17 lymphomas) using ANNs in a complete leaveone-out analysis demonstrated that all except one sample were accurately diagnosed as their respective category. Moreover, using an ANN-based gene minimization strategy in a separate analysis, we found that the top 31 genes could correctly diagnose all 96 tumors. Our results suggest that this molecular test based on a multiplex PCR reaction may assist the physician in the rapid confirmation of the diagnosis of these cancers. (J Mol Diagn 2007, 9
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