Role of adenine functional groups in the recognition of the 3′-splice-site AG during the second step of pre-mRNA splicing

The AG dinucleotide at the 3′ splice sites of metazoan nuclear pre-mRNAs plays a critical role in catalytic step II of the splicing reaction. Previous studies have shown that replacement of the guanine by adenine in the AG (AG → GG) inhibits this step. We find that the second step was even more severely inhibited by cytosine (AG → CG) or uracil (AG → UG) substitutions at this position. By contrast, a relatively moderate inhibition was observed with a hypoxanthine substitution (AG → HG). When adenine was replaced by a purine base (AG → PG) or by 7-deazaadenine (AG → c7AG), little effect on the second step was observed, suggesting that the 6-NH2 and N7 groups do not play a critical role in adenine recognition. Finally, replacement of adenine by 2-aminopurine (AG → 2-APG) had no effect on the second step. Taken together, our results suggest that the N1 group of adenine functions as an essential determinant in adenine recognition during the second step of pre-mRNA splicing.

Plant regeneration functional groups modulate the response to fire of soil enzyme activities in a Mediterranean shrubland

Soil enzymes are critical to soil nutrient cycling function but knowledge on the factors that control their response to major disturbances such as wildfires remains very limited. We evaluated the effect of fire-related plant functional traits (resprouting and seeding) on the resistance and resilience to fire of two soil enzyme activities involved in phosphorus and carbon cycling (acid phosphatase and β-glucosidase) in a Mediterranean shrublands in SE Spain. Using experimental fires, we compared four types of shrubland microsites: SS (vegetation patches dominated by seeder species), RR (patches dominated by resprouter species), SR (patches co-dominated by seeder and resprouter species), and IP (shrub interpatches). We assessed pre- and post-fire activities of the target soil enzymes, available P, soil organic C, and plant cover dynamics over three years after the fire. Post-fire regeneration functional groups (resprouter, seeder) modulated both pre- and post-fire activity of acid phosphatase and β-glucosidase, with higher activity in RR and SR patches than in SS patches and IP. However, we found no major differences in enzyme resistance and resilience between microsite types, except for a trend towards less resilience in SS patches. Fire similarly reduced the activity of both enzymes. However, acid phosphatase and β-glucosidase showed contrasting post-fire dynamics. While β-glucosidase proved to be rather resilient to fire, fully recovering three years after fire, acid phosphatase showed no signs of recovery in that period. Overall, the results indicate a positive influence of resprouter species on soil enzyme activity that is very resistant to fire. Long-lasting decrease in acid phosphatase activity probably resulted from the combined effect of P availability and post-fire drought. Our results provide insights on how plant functional traits modulate soil biochemical and microbiological response to fire in Mediterranean fire-prone shrublands.

Cocrystallisation involving the thioamide, amide and imide functional groups

The work presented in this dissertation focused on the development and characterisation of novel cocrystals that incorporated the thioamide, amide and imide functional groups. A particular emphasis was placed on the characterisation of these cocrystals by single crystal X-ray diffraction methods. In Chapter One a summary of the intermolecular interactions utilised in this work and a short review of the solid state and multicomponent systems is provided. A brief introduction to the ways in which different multicomponent systems can be distinguished, crystal engineering strategies and a number of cocrystal applications highlights the importance the understanding of intermolecular interactions can have on the physical and chemical properties of crystalline materials. Chapter Two is the first Results and Discussion chapter and includes an introduction that is specific to the chapter. The main body of this work focuses on the primary aromatic thioamide functional group and its propensity to cocrystallise with a number of sulfoxides. Unlike the amide functional group, thioamides are not commonly employed in cocrystallisation studies. This chapter presents the first direct comparison between the cocrystallisation abilities of these two functional groups and the intermolecular hydrogen bonding interactions present in the cocrystal structures are examined. Chapter Three describes the crystal landscape of a short series of secondary aromatic amides and their analogous thioamides. Building on the results obtained in Chapter Two, a cocrystal screen of the secondary thioamides with the sulfoxide functional group was carried out in order to determine the effect removing a hydrogen bond had on the supramolecular synthons observed in the cocrystals. These secondary thioamides are also utilised in Chapter Four, which examines their halogen bonding capabilities with two organoiodine coformers: 1,2- and 1,4-diiodotetrafluorobenzene. Chapter Five explores the cocrystallisation abilities of three related cyclic imides as coformers for cocrystallisation with a range of commonly used coformers. Chapter Six is an overall conclusions chapter that highlights the findings of the results presented in Chapters Two to Five. Chapter Seven details the instrument and experimental data for the compounds and cocrystals discussed in the Results and Discussion Chapters. The accompanying CD contains all of the crystallographic data in .cif format for the novel single crystal structures characterised in this work.

Improvement of carbon materials performance by nitrogen functional groups in electrochemical capacitors in organic electrolyte at severe conditions

N-doped activated carbon fibers have been synthesized by using chemically polymerized aniline as source of nitrogen. Commercial activated carbon fibers (A20) were chemically modified with a thin film of polyaniline (PANI) inside the microporosity of the carbon fibers. The modified activated carbon fibers were carbonized at 600 and 800 °C, respectively. In this way, activated carbon fibers modified with surface nitrogen species were prepared in order to analyze their influence in the performance of electrochemical capacitors in organic electrolyte. Symmetric capacitors were made of activated carbon fibers and N-doped activated carbon fibers and tested in a two-electrode cell configuration, using triethylmethylammonium tetrafluoroborate/propylene carbonate (TEMA-BF4/PC) as electrolyte. The effect of nitrogen species in the degradation or stabilization of the capacitor has been analyzed through floating durability tests using a high voltage charging (3.2 V). The results show higher stabilizing effect in carbonized samples (N-ACF) than in non-carbonized samples and pristine activated carbon fibers, which is attributed to the presence of aromatic nitrogen group, especially positively charged N-functional groups.

Biological significance of dead biomass retention trait in Mediterranean Basin species: an analysis between different successional niches and regeneration strategies as functional groups

Standing dead biomass retention is considered one of the most relevant fuel structural traits to affect plant flammability. However, very little is known about the biological significance of this trait and its distribution between different functional groups. Our aim was to analyse how the proportion of dead biomass produced in Mediterranean species is related to the successional niche of species (early-, mid- and late-successional stages) and the regeneration strategy of species (seeders and resprouters). We evaluated biomass distribution by size classes and standing dead biomass retention in nine dominant species from the Mediterranean Basin in different development stages (5, 9, 14 and 26 years since the last fire). The results revealed significant differences in the standing dead biomass retention of species that presented a distinct successional niche or regeneration strategy. These differences were restricted to the oldest ages studied (>9 years). Tree and small tree resprouters, typical in late-successional stages, presented slight variations with age and a less marked trend to retain dead biomass, while seeder shrubs and dwarf shrubs, characteristic of early-successional stages, showed high dead biomass loads. Our results suggest that the species that tend to retain more dead branches are colonising species that may promote fire in early-successional stages.

Species that share traits do not necessarily form distinct and universally applicable functional effect groups

Peer reviewed

Potentiometric quantification and speciation of oxygenated groups in humic substances using BEST7 software

In this study the BEST7 software was employed to quantify different classes of functional groups and to model the proton titration behavior of humic substances. To illustrate the process, the Suwannee River fulvic acid of the IHSS (International Humic Substances Society) was used. Five categories - two classes of phenolic groups (phenol and cathecol), two classes of carboxylic groups (benzoic and phtalic) and the combination between them (salicylic) - of oxygenated groups were considered as being responsible for the potentiometric behavior of the sample and were quantitatively determined. The most and the least abundant groups were cathecol (3.300 ± 0.010 mmol g-1) and phenol (1.225 ± 0.070 mmol g-1), respectively. The estimated equilibrium constants were also determined and were in good agreement with the literature values for phenol and cathecol groups and for benzoic, phtalic and salicylic acids. Distribution diagrams of the species were generated with the software SPE and SPEPLOT.

Network connectance and autonomy analyses of the photosynthetic apparatus in tropical tree species from different successional groups under contrasting irradiance conditions

Biological systems are complex dynamical systems whose relationships with environment have strong implications on their regulation and survival. From the interactions between plant and environment can emerge a quite complex network of plant responses rarely observed through classical analytical approaches. The objective of this current study was to test the hypothesis that photosynthetic responses of different tree species to increasing irradiance are related to changes in network connectances of gas exchange and photochemical apparatus, and alterations in plant autonomy in relation to the environment. The heat dissipative capacity through daily changes in leaf temperature was also evaluated. It indicated that the early successional species (Citharexylum myrianthum Cham. and Rhamnidium elaeocarpum Reiss.) were more efficient as dissipative structures than the late successional one (Cariniana legalis (Mart.) Kuntze), suggesting that the parameter deltaT (T ºCair - T ºCleaf) could be a simple tool in order to help the classification of successional classes of tropical trees. Our results indicated a pattern of network responses and autonomy changes under high irradiance. Considering the maintenance of daily CO2 assimilation, the tolerant species (C. myrianthum and R. elaeocarpum) to high irradiance trended to maintain stable the level of gas exchange network connectance and to increase the autonomy in relation to the environment. On the other hand, the late successional species (C. legalis) trended to lose autonomy, decreasing the network connectance of gas exchange. All species showed lower autonomy and higher network connectance of the photochemical apparatus under high irradiance.

Photosynthetic responses of tropical tree species from different successional groups under contrasting irradiance conditions

This study evaluated the photosynthetic responses of seven tropical trees of different successional groups under contrasting irradiance conditions, taking into account changes in gas exchange and chlorophyll a fluorescence. Although early successional species have shown higher values of CO2 assimilation (A) and transpiration (E), there was not a defined pattern of the daily gas exchange responses to high irradiance (FSL) among evaluated species. Cariniana legalis (Mart.) Kuntze (late secondary) and Astronium graveolens Jacq. (early secondary) exhibited larger reductions in daily-integrated CO2 assimilation (DIA) when transferred from medium light (ML) to FSL. On the other hand, the pioneer species Guazuma ulmifolia Lam. had significant DIA increase when exposed to FSL. The pioneers Croton spp. trended to show a DIA decrease around 19%, while Cytharexyllum myrianthum Cham. (pioneer) and Rhamnidium elaeocarpum Reiss. (early secondary) trended to increase DIA when transferred to FSL. Under this condition, all species showed dynamic photoinhibition, except for C. legalis that presented chronic photoinhibition of photosynthesis. Considering daily photosynthetic processes, our results supported the hypothesis of more flexible responses of early successional species (pioneer and early secondary species). The principal component analysis indicated that the photochemical parameters effective quantum efficiency of photosystem II and apparent electron transport rate were more suitable to separate the successional groups under ML condition, whereas A and E play a major role to this task under FSL condition.

GABA and 5-HT chitosan nanoparticles enhanced liver cell proliferation and neuronal survival in partially hepatectomised rats: GABAB and 5-HT2A receptors functional

Nanoparticulate drug delivery systems provide wide opportunities for solving problems associated with drug stability or disease states and create great expectations in the area of drug delivery (Bosselmann & Williams, 2012). Nanotechnology, in a simple way, explains the technology that deals with one billionth of a meter scale (Ochekpe, et al., 2009). Fewer side effects, poor bioavailability, absorption at intestine, solubility, specific delivery to site of action with good pharmacological efficiency, slow release, degradation of drug and effective therapeutic outcome, are the major challenges faced by most of the drug delivery systems. To a great extent, biopolymer coated drug delivery systems coupled with nanotechnology alleviate the major drawbacks of the common delivery methods. Chitosan, deacetylated chitin, is a copolymer of β-(1, 4) linked glucosamine (deacetylated unit) and N- acetyl glucosamine (acetylated unit) (Radhakumary et al., 2005). Chitosan is biodegradable, non-toxic and bio compatible. Owing to the removal of acetyl moieties that are present in the amine functional groups of chitin, chitosan is readily soluble in aqueous acidic solution. The solubilisation occurs through the protonation of amino groups on the C-2 position of D-glucosamine residues whereby polysaccharide is converted into polycation in acidic media. Chitosan interacts with many active compounds due to the presence of amine group in it. The presence of this active amine group in chitosan was exploited for the interaction with the active molecules in the present study. Nanoparticles of chitosan coupled drugs are utilized for drug delivery in eye, brain, liver, cancer tissues, treatment of spinal cord injury and infections (Sharma et al., 2007; Li, et a., 2009; Paolicelli et al., 2009; Cho et al., 2010). To deliver drugs directly to the intended site of action and to improve pharmacological efficiency by minimizing undesired side effects elsewhere in the body and decrease the long-term use of many drugs, polymeric drug delivery systems can be used (Thatte et al., 2005).

Plant species and functional group effects on abiotic and microbial soil properties and plant-soil feedback responses in two grasslands

1 Plant species differ in their capacity to influence soil organic matter, soil nutrient availability and the composition of soil microbial communities. Their influences on soil properties result in net positive or negative feedback effects, which influence plant performance and plant community composition. 2 For two grassland systems, one on a sandy soil in the Netherlands and one on a chalk soil in the United Kingdom, we investigated how individual plant species grown in monocultures changed abiotic and biotic soil conditions. Then, we determined feedback effects of these soils to plants of the same or different species. Feedback effects were analysed at the level of plant species and plant taxonomic groups (grasses vs. forbs). 3 In the sandy soils, plant species differed in their effects on soil chemical properties, in particular potassium levels, but PLFA (phospholipid fatty acid) signatures of the soil microbial community did not differ between plant species. The effects of soil chemical properties were even greater when grasses and forbs were compared, especially because potassium levels were lower in grass monocultures. 4 In the chalk soil, there were no effects of plant species on soil chemical properties, but PLFA profiles differed significantly between soils from different monocultures. PLFA profiles differed between species, rather than between grasses and forbs. 5 In the feedback experiment, all plant species in sandy soils grew less vigorously in soils conditioned by grasses than in soils conditioned by forbs. These effects correlated significantly with soil chemical properties. None of the seven plant species showed significant differences between performance in soil conditioned by the same vs. other plant species. 6 In the chalk soil, Sanguisorba minor and in particular Briza media performed best in soil collected from conspecifics, while Bromus erectus performed best in soil from heterospecifics. There was no distinctive pattern between soils collected from forb and grass monocultures, and plant performance could not be related to soil chemical properties or PLFA signatures. 7 Our study shows that mechanisms of plant-soil feedback can depend on plant species, plant taxonomic (or functional) groups and site-specific differences in abiotic and biotic soil properties. Understanding how plant species can influence their rhizosphere, and how other plant species respond to these changes, will greatly enhance our understanding of the functioning and stability of ecosystems.

Diversity of functional traits of fleshy fruits in a species-rich Atlantic rain forest

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)