Skeletal trade-offs in coralline algae in response to ocean acidification

Ocean acidification is changing the marine environment, with potentially serious consequences for many organisms. Much of our understanding of ocean acidification effects comes from laboratory experiments, which demonstrate physiological responses over relatively short timescales. Observational studies and, more recently, experimental studies in natural systems suggest that ocean acidification will alter the structure of seaweed communities. Here, we provide a mechanistic understanding of altered competitive dynamics among a group of seaweeds, the crustose coralline algae (CCA). We compare CCA from historical experiments (1981-1997) with specimens from recent, identical experiments (2012) to describe morphological changes over this time period, which coincides with acidification of seawater in the Northeastern Pacific. Traditionally thick species decreased in thickness by a factor of 2.0-2.3, but did not experience a change in internal skeletal metrics. In contrast, traditionally thin species remained approximately the same thickness but reduced their total carbonate tissue by making thinner inter-filament cell walls. These changes represent alternative mechanisms for the reduction of calcium carbonate production in CCA and suggest energetic trade-offs related to the cost of building and maintaining a calcium carbonate skeleton as pH declines. Our classification of stress response by morphological type may be generalizable to CCA at other sites, as well as to other calcifying organisms with species-specific differences in morphological types.

Calcification of the Arctic coralline red algae Lithothamnion glaciale in response to elevated CO2

Rising atmospheric CO2 concentrations could cause a calcium carbonate subsaturation of Arctic surface waters in the next 20 yr, making these waters corrosive for calcareous organisms. It is presently unknown what effects this will have on Arctic calcifying organisms and the ecosystems of which they are integral components. So far, acidification effects on crustose coralline red algae (CCA) have only been studied in tropical and Mediterranean species. In this work, we investigated calcification rates of the CCA Lithothamnion glaciale collected in northwest Svalbard in laboratory experiments under future atmospheric CO2 concentrations. The algae were exposed to simulated Arctic summer and winter light conditions in 2 separate experiments at optimum growth temperatures. We found a significant negative effect of increased CO2 levels on the net calcification rates of L. glaciale in both experiments. Annual mean net dissolution of L. glaciale was estimated to start at an aragonite saturation state between 1.1 and 0.9 which is projected to occur in parts of the Arctic surface ocean between 2030 and 2050 if emissions follow 'business as usual' scenarios (SRES A2; IPCC 2007). The massive skeleton of CCA, which consist of more than 80% calcium carbonate, is considered crucial to withstanding natural stresses such as water movement, overgrowth or grazing. The observed strong negative response of this Arctic CCA to increased CO2 levels suggests severe threats of the projected ocean acidification for an important habitat provider in the Arctic coastal ocean.

Contrasting effects of ocean acidification on tropical fleshy and calcareous algae

Despite the heightened awareness of ocean acidification (OA) effects on marine organisms, few studies empirically juxtapose biological responses to CO2 manipulations across functionally distinct primary producers, particularly benthic algae. Algal responses to OA may vary because increasing CO2 has the potential to fertilize photosynthesis but impair biomineralization. Using a series of repeated experiments on Palmyra Atoll, simulated OA effects were tested across a suite of ecologically important coral reef algae, including five fleshy and six calcareous species. Growth, calcification and photophysiology were measured for each species independently and metrics were combined from each experiment using a meta-analysis to examine overall trends across functional groups categorized as fleshy, upright calcareous, and crustose coralline algae (CCA). The magnitude of the effect of OA on algal growth response varied by species, but the direction was consistent within functional groups. Exposure to OA conditions generally enhanced growth in fleshy macroalgae, reduced net calcification in upright calcareous algae, and caused net dissolution in CCA. Additionally, three of the five fleshy seaweeds tested became reproductive upon exposure to OA conditions. There was no consistent effect of OA on algal photophysiology. Our study provides experimental evidence to support the hypothesis that OA will reduce the ability of calcareous algae to biomineralize. Further, we show that CO2 enrichment either will stimulate population or somatic growth in some species of fleshy macroalgae. Thus, our results suggest that projected OA conditions may favor non-calcifying algae and influence the relative dominance of fleshy macroalgae on reefs, perpetuating or exacerbating existing shifts in reef community structure.

RNase E is required for the maturation of ssrA RNA and normal ssrA RNA peptide-tagging activity

During recent studies of ribonucleolytic “degradosome” complexes of Escherichia coli, we found that degradosomes contain certain RNAs as well as RNase E and other protein components. One of these RNAs is ssrA (for small stable RNA) RNA (also known as tm RNA or 10Sa RNA), which functions as both a tRNA and mRNA to tag the C-terminal ends of truncated proteins with a short peptide and target them for degradation. Here, we show that mature 363-nt ssrA RNA is generated by RNase E cleavage at the CCA-3′ terminus of a 457-nt ssrA RNA precursor and that interference with this cleavage in vivo leads to accumulation of the precursor and blockage of SsrA-mediated proteolysis. These results demonstrate that RNase E is required to produce mature ssrA RNA and for normal ssrA RNA peptide-tagging activity. Our findings indicate that RNase E, an enzyme already known to have a central role in RNA processing and decay in E. coli, also has the previously unsuspected ability to affect protein degradation through its role in maturation of the 3′ end of ssrA RNA.

Oligonucleotide-directed peptide synthesis in a ribosome- and ribozyme-free system

Peptide bond formation by the ribosome requires 23S rRNA and its interaction with the 3′-CCA end of tRNA. To investigate the possible evolutionary development of the peptidyl transfer reaction, we tried to obtain peptide bond formation without the ribosome or rRNA simply by using a piece of tRNA—an aminoacyl-minihelix—mixed with sequence-specific oligonucleotides that contained puromycin. Peptide bond formation was detected by gel electrophoresis, TLC analysis, and mass spectrometry. Peptide synthesis depended on sequence complementarity between the 3′-CCA sequence of the minihelix and the puromycin-bearing oligonucleotide. However, proximity of the reacting species was not by itself sufficient for peptide bond formation. In addition, imidazole as a catalyst was required. Its role may be similar to the recently proposed mechanism, wherein A2451 of 23S rRNA works as a general base. Thus, peptide bond formation can be achieved with a simple, minimized system that captures the essence of an interaction seen in the ribosome.

Probing of tertiary interactions in RNA: 2'-hydroxyl-base contacts between the RNase P RNA and pre-tRNA.

A general method has been developed to analyze all 2' hydroxyl groups involved in tertiary interactions in RNA in a single experiment. This method involves comparing the activity of populations of circularly permuted RNAs that contain or lack potential hydrogen-bond donors at each position. The 2' hydroxyls of the pre-tRNA substrate identified as potential hydrogen bond donors in intermolecular interactions with the ribozyme from eubacterial RNase P (P RNA) are located in the T stem and T loop, acceptor stem, and 3' CCA regions. To locate the hydrogen-bond acceptors for one of those 2' hydroxyls in the P RNA, a phylogenetically conserved adenosine was mutated to a guanosine. When this mutant P RNA was used, increased cleavage activity of a single circularly permuted substrate within the population was observed. The cleavage efficiency (kcat/Km) of a singly 2'-deoxy-substituted substrate at this position in the T stem was also determined. For the wild-type P RNA, the catalytic efficiency was significantly decreased compared with that of the all-ribo substrate, consistent with the notion that this 2' hydroxyl plays an important role. For the P RNA mutant, no additional effect was found upon 2'-deoxy substitution. We propose that this particular 2' hydroxyl in the pre-tRNA interacts specifically with this adenosine in the P RNA. This method should be useful in examining the role of 2' hydroxyl groups in other RNA-RNA and RNA-protein complexes.

Precursor of C4 antisense RNA of bacteriophages P1 and P7 is a substrate for RNase P of Escherichia coli.

The C4 repressor of the temperate bacteriophages P1 and P7 inhibits antirepressor (Ant) synthesis and is essential for establishment and maintenance of lysogeny. C4 is an antisense RNA acting on a target, Ant mRNA, which is transcribed from the same promoter. The antisense-target RNA interaction requires processing of C4 RNA from a precursor RNA. Here we show that 5' maturation of C4 RNA in vivo depends on RNase P. In vitro, Escherichia coli RNase P and its catalytic RNA subunit (M1 RNA) can generate the mature 5' end of C4 RNA from P1 by a single endonucleolytic cut, whereas RNase P from the E. coli rnpA49 mutant, carrying a missense mutation in the RNase P protein subunit, is defective in the 5' maturation of C4 RNA. Primer extension analysis of RNA transcribed in vivo from a plasmid carrying the P1 c4 gene revealed that 5'-mature C4 RNA was the predominant species in rnpA+ bacteria, whereas virtually no mature C4 RNA was found in the temperature-sensitive rnpA49 strain at the restrictive temperature. Instead, C4 RNA molecules carrying up to five extra nucleotides beyond the 5' end accumulated. The same phenotype was observed in rnpA+ bacteria which harbored a plasmid carrying a P7 c4 mutant gene with a single C-->G base substitution in the structural homologue to the CCA 3' end of tRNAs. Implications of C4 RNA processing for the lysis/lysogeny decision process of bacteriophages P1 and P7 are discussed.

Síntese, caracterização e modificação de superfícies de sílicas mesoporosas ordenadas para captura de CO2

Processos como a purificação do metano (CH4) e a produção de hidrogênio gasoso (H2) envolvem etapas de separação de CO2. Atualmente, etanolaminas como monoetanolamina (MEA), dietanolamina (DEA), metildietanolamina (MDEA) e trietanolamina (TEA) são as substâncias mais utilizadas no processo de separação/captura de CO2 em processos industriais. Entretanto, o uso destas substâncias apresenta alguns inconvenientes devido à alta volatilidade, dificuldade de se trabalhar com material líquido, também ao alto gasto energético envolvido das etapas de regeneração e à baixa estabilidade térmica e química. Com base nessa problemática, esse trabalho teve por objetivo a síntese de um tipo de sílica mesoporosa altamente ordenada (SBA-15) de modo a utilizá-la no processo de captura de CO2. O trabalho foi dividido em quatro etapas experimentais que envolveram a síntese da SBA-15, o estudo do comportamento térmico de algumas etanolaminas livres, síntese e caracterização de materiais adsorventes preparados a partir de incorporação de etanolaminas à SBA-15 e estudo da eficiência de captura de CO2 por esses materiais. Novas alternativas de síntese da SBA-15 foram estudadas neste trabalho, visando aperfeiçoar as propriedades texturais do material produzido. Tais alternativas são baseadas na remoção do surfatante, utilizado como molde na síntese da sílica mesoporosa, por meio da extração por Soxhlet, utilizando diferentes solventes. O processo contribuiu para melhorar as propriedades do material obtido, evitando o encolhimento da estrutura que pode ser ocasionado durante a etapa de calcinação. Por meio de técnicas como TG/DTG, DSC, FTIR e Análise Elementar de C, H e N foi realizada a caracterização físico-química e termoanalítica da MEA, DEA, MDEA e TEA, visando melhor conhecer as características destas substâncias. Estudos cinéticos baseados nos métodos termogravimétricos isotérmicos e não isotérmicos (Método de Ozawa) foram realizados, permitindo a determinação de parâmetros cinéticos envolvidos nas etapas de volatilização/decomposição térmica das etanolaminas. Além das técnicas acima mencionadas, MEV, MET, SAXS e Medidas de Adsorção de N2 foram utilizadas na caraterização da SBA-15 antes e após a incorporação das etanolaminas. Dentre as etanolaminas estudadas, a TEA apresentou maior estabilidade térmica, entretanto, devido ao seu maior impedimento estérico, é a etanolamina que apresenta menor afinidade com o CO2. Diferentemente das demais etanolaminas estudadas, a decomposição térmica da DEA envolve uma reação intramolecular, levando a formação de MEA e óxido de etileno. A incorporação destes materiais à SBA-15 aumentou a estabilidade térmica das etanolaminas, uma vez que parte do material permanece dentro dos poros da sílica. Os ensaios de adsorção de CO2 mostraram que a incorporação da MEA à SBA-15 catalisou o processo de decomposição térmica da mesma. A MDEA foi a etanolamina que apresentou maior poder de captura de CO2 e sua estabilidade térmica foi consideravelmente aumentada quando a mesma foi incorporada à SBA-15, aumentando também seu potencial de captura de CO2.

Evolução estrutural e performance catalítica de nanopartículas de AuPd de composição variável

Nanopartículas bimetálicas de AuPd têm mostrado excelente atividade catalítica em reações de oxidação. O entendimento dos efeitos da variação da composição e morfologia das nanopartículas bimetálicas em suas propriedades catalíticas é fundamental para a preparação de catalisadores cada vez mais ativos e seletivos. Neste trabalho foram estudadas nanopartículas bimetálicas de AuPd de composição variável suportadas sobre um suporte constituído por nanopartículas de magnetita revestidas por sílica. O efeito da calcinação e da redução com hidrogênio sobre a morfologia e composição das nanopartículas bimetálicas foi acompanhado pelas técnicas de TEM, XEDS, XAS, XRD e XPS. A correlação entre estrutura, composição e atividade catalítica dos catalisadores preparados foi estudada pelo acompanhamento de reações de oxidação de monóxido de carbono e de oxidação de álcool benzílico. As amostras não calcinadas apresentaram segregação metálica em todas as composições estudadas. Após a etapa de calcinação, maior segregação metálica foi encontrada, com a formação de óxido de paládio na superfície das nanopartículas, exceto na amostra mais rica em ouro. O tratamento das amostras oxidadas com hidrogênio foi capaz de reduzir os metais oxidados na superfície das nanopartículas, mas um enriquecimento em paládio na superfície e maior segregação entre ouro e paládio foram observados. Uma melhora na atividade catalítica na oxidação de monóxido de carbono foi observada juntamente com um aumento na composição de paládio, além disso, observou-se uma maior atividade catalítica em relação às nanopartículas não calcinadas para as amostras calcinadas e reduzidas. Para a oxidação de álcool benzílico um aumento na atividade catalítica de até cinco vezes foi observado após a calcinação dos catalisadores, com maior atividade para a amostra de composição Au1Pd2. A queda na atividade catalítica após a redução dos catalisadores mostrou que a presença de óxido de paládio na superfície das nanopartículas é fundamental para que seja observada uma maior atividade catalítica.