CIRCULATION AND SUSPENDED PARTICULATE MATTER TRANSPORT IN A TIDALLY DOMINATED ESTUARY: CARAVELAS ESTUARY, BAHIA, BRAZIL

The circulation and transport of suspended particulate matter in the Caravelas Estuary are assessed. Nearly-synoptic hourly hydrographic, current (ADCP velocity and volume transport) and suspended particulate matter data were collected during a full semidiurnal spring tide, on the two transects Boca do Tomba and Barra Velha and on longitudinal sections at low and high tide. On the first transect the peak ebb currents (-1.5 ms(-1)) were almost twice as strong as those of the wider and shallow Barra Velha inlet (-0.80 ms(-1)) and the peak flood currents were 0.75 and 0.60 ms(-1), respectively. Due to the strong tidal currents both inlets had weak vertical salinity stratification and were classified with the Stratification-circulation Diagram as Type 2a (partially mixed-weakly stratified) and Type 1a (well mixed). Volume transports were very close, ranging from -3,500 to 3,100 m(3)s(-1) at the ebb and flood, respectively, with a residual -630 m(3)s(-1). The concentration of the suspended particulate matter was closely related to the tidal variation and decreased landwards from 50 mg. L(-1) at the estuary mouth, to 10 mg.L(-1) at distances of 9 and 16 km for the low and high tide experiments, respectively. The total residual SPM transport was out of the estuary at rates of -18 tons per tidal cycle.

Structural and Functional Insights from the Metagenome of an Acidic Hot Spring Microbial Planktonic Community in the Colombian Andes

A taxonomic and annotated functional description of microbial life was deduced from 53 Mb of metagenomic sequence retrieved from a planktonic fraction of the Neotropical high Andean (3,973 meters above sea level) acidic hot spring El Coquito (EC). A classification of unassembled metagenomic reads using different databases showed a high proportion of Gammaproteobacteria and Alphaproteobacteria (in total read affiliation), and through taxonomic affiliation of 16S rRNA gene fragments we observed the presence of Proteobacteria, micro-algae chloroplast and Firmicutes. Reads mapped against the genomes Acidiphilium cryptum JF-5, Legionella pneumophila str. Corby and Acidithiobacillus caldus revealed the presence of transposase-like sequences, potentially involved in horizontal gene transfer. Functional annotation and hierarchical comparison with different datasets obtained by pyrosequencing in different ecosystems showed that the microbial community also contained extensive DNA repair systems, possibly to cope with ultraviolet radiation at such high altitudes. Analysis of genes involved in the nitrogen cycle indicated the presence of dissimilatory nitrate reduction to N2 (narGHI, nirS, norBCDQ and nosZ), associated with Proteobacteria-like sequences. Genes involved in the sulfur cycle (cysDN, cysNC and aprA) indicated adenylsulfate and sulfite production that were affiliated to several bacterial species. In summary, metagenomic sequence data provided insight regarding the structure and possible functions of this hot spring microbial community, describing some groups potentially involved in the nitrogen and sulfur cycling in this environment. Citation: Jimenez DJ, Andreote FD, Chaves D, Montana JS, Osorio-Forero C, et al. (2012) Structural and Functional Insights from the Metagenome of an Acidic Hot Spring Microbial Planktonic Community in the Colombian Andes. PLoS ONE 7(12): e52069. doi:10.1371/journal.pone.0052069

SmTRC1, a novel Schistosoma mansoni DNA transposon, discloses new families of animal and fungi transposons belonging to the CACTA superfamily

Abstract Background The CACTA (also called En/Spm) superfamily of DNA-only transposons contain the core sequence CACTA in their Terminal Inverted Repeats (TIRs) and so far have only been described in plants. Large transcriptome and genome sequence data have recently become publicly available for Schistosoma mansoni, a digenetic blood fluke that is a major causative agent of schistosomiasis in humans, and have provided a comprehensive repository for the discovery of novel genes and repetitive elements. Despite the extensive description of retroelements in S. mansoni, just a single DNA-only transposon belonging to the Merlin family has so far been reported in this organism. Results We describe a novel S. mansoni transposon named SmTRC1, for S. mansoni Transposon Related to CACTA 1, an element that shares several characteristics with plant CACTA transposons. Southern blotting indicates approximately 30–300 copies of SmTRC1 in the S. mansoni genome. Using genomic PCR followed by cloning and sequencing, we amplified and characterized a full-length and a truncated copy of this element. RT-PCR using S. mansoni mRNA followed by cloning and sequencing revealed several alternatively spliced transcripts of this transposon, resulting in distinct ORFs coding for different proteins. Interestingly, a survey of complete genomes from animals and fungi revealed several other novel TRC elements, indicating new families of DNA transposons belonging to the CACTA superfamily that have not previously been reported in these kingdoms. The first three bases in the S. mansoni TIR are CCC and they are identical to those in the TIRs of the insects Aedes aegypti and Tribolium castaneum, suggesting that animal TRCs may display a CCC core sequence. Conclusion The DNA-only transposable element SmTRC1 from S. mansoni exhibits various characteristics, such as generation of multiple alternatively-spliced transcripts, the presence of terminal inverted repeats at the extremities of the elements flanked by direct repeats and the presence of a Transposase_21 domain, that suggest a distant relationship to CACTA transposons from Magnoliophyta. Several sequences from other Metazoa and Fungi code for proteins similar to those encoded by SmTRC1, suggesting that such elements have a common ancestry, and indicating inheritance through vertical transmission before separation of the Eumetazoa, Fungi and Plants.

Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes

Abstract Background Sugarcane (Saccharum spp.) has become an increasingly important crop for its leading role in biofuel production. The high sugar content species S. officinarum is an octoploid without known diploid or tetraploid progenitors. Commercial sugarcane cultivars are hybrids between S. officinarum and wild species S. spontaneum with ploidy at ~12×. The complex autopolyploid sugarcane genome has not been characterized at the DNA sequence level. Results The microsynteny between sugarcane and sorghum was assessed by comparing 454 pyrosequences of 20 sugarcane bacterial artificial chromosomes (BACs) with sorghum sequences. These 20 BACs were selected by hybridization of 1961 single copy sorghum overgo probes to the sugarcane BAC library with one sugarcane BAC corresponding to each of the 20 sorghum chromosome arms. The genic regions of the sugarcane BACs shared an average of 95.2% sequence identity with sorghum, and the sorghum genome was used as a template to order sequence contigs covering 78.2% of the 20 BAC sequences. About 53.1% of the sugarcane BAC sequences are aligned with sorghum sequence. The unaligned regions contain non-coding and repetitive sequences. Within the aligned sequences, 209 genes were annotated in sugarcane and 202 in sorghum. Seventeen genes appeared to be sugarcane-specific and all validated by sugarcane ESTs, while 12 appeared sorghum-specific but only one validated by sorghum ESTs. Twelve of the 17 sugarcane-specific genes have no match in the non-redundant protein database in GenBank, perhaps encoding proteins for sugarcane-specific processes. The sorghum orthologous regions appeared to have expanded relative to sugarcane, mostly by the increase of retrotransposons. Conclusions The sugarcane and sorghum genomes are mostly collinear in the genic regions, and the sorghum genome can be used as a template for assembling much of the genic DNA of the autopolyploid sugarcane genome. The comparable gene density between sugarcane BACs and corresponding sorghum sequences defied the notion that polyploidy species might have faster pace of gene loss due to the redundancy of multiple alleles at each locus.

Avaliação da influência de condições meteorológicas na ocorrência e manutenção de um episódio prolongado com altas concentrações de ozônio sobre a região metropolitana de São Paulo

Na Região Metropolitana de São Paulo, a rede de monitoramento da qualidade do ar registra frequentemente valores de concentração de ozônio superiores aos estabelecidos pela legislação em vigor no Brasil. Em algumas ocasiões, condições meteorológicas favoráveis ao processo de formação de ozônio possibilitam a ocorrência de altas concentrações de ozônio durante diversos dias consecutivos na região. A influência de condições meteorológicas no episódio de poluição, registrado entre os dias de 24 de fevereiro e 05 de março de 2003, foi avaliada através de simulações numéricas com o modelo SPM-BRAMS. Estudos observacionais mostram que a ocorrência de ventos fracos, principalmente, durante o período noturno e durante as manhãs, favorece a formação de altas concentrações de ozônio sobre a região. O horário de entrada e a atuação da brisa marítima são fundamentais para o transporte do ozônio e de seus precursores. Essas condições foram bem simuladas pelo modelo. Para os dias mais críticos, quando diversas estações de monitoramento registraram a ocorrência de violações ao padrão nacional de qualidade do ar, o modelo simulou adequadamente as condições atmosféricas determinantes para a manutenção de valores elevados nas concentrações de ozônio, sem a necessidade de nenhum procedimento artificial ao longo das integrações.