DNA alignment and Bayesian trees of partial sequences of COI, COIII and the haemocyanin functional unit f-g of 28 octopod species

Background: Octopods have successfully colonised the world's oceans from the tropics to the poles. Yet, successful persistence in these habitats has required adaptations of their advanced physiological apparatus to compensate impaired oxygen supply. Their oxygen transporter haemocyanin plays a major role in cold tolerance and accordingly has undergone functional modifications to sustain oxygen release at sub-zero temperatures. However, it remains unknown how molecular properties evolved to explain the observed functional adaptations. We thus aimed to assess whether natural selection affected molecular and structural properties of haemocyanin that explains temperature adaptation in octopods. Results: Analysis of 239 partial sequences of the haemocyanin functional units (FU) f and g of 28 octopod species of polar, temperate, subtropical and tropical origin revealed natural selection was acting primarily on charge properties of surface residues. Polar octopods contained haemocyanins with higher net surface charge due to decreased glutamic acid content and higher numbers of basic amino acids. Within the analysed partial sequences, positive selection was present at site 2545, positioned between the active copper binding centre and the FU g surface. At this site, methionine was the dominant amino acid in polar octopods and leucine was dominant in tropical octopods. Sites directly involved in oxygen binding or quaternary interactions were highly conserved within the analysed sequence. Conclusions: This study has provided the first insight into molecular and structural mechanisms that have enabled octopods to sustain oxygen supply from polar to tropical conditions. Our findings imply modulation of oxygen binding via charge-charge interaction at the protein surface, which stabilize quaternary interactions among functional units to reduce detrimental effects of high pH on venous oxygen release. Of the observed partial haemocyanin sequence, residue 2545 formed a close link between the FU g surface and the active centre, suggesting a role as allosteric binding site. The prevalence of methionine at this site in polar octopods, implies regulation of oxygen affinity via increased sensitivity to allosteric metal binding. High sequence conservation of sites directly involved in oxygen binding indicates that functional modifications of octopod haemocyanin rather occur via more subtle mechanisms, as observed in this study.

Negative effects of ocean acidification on two crustose coralline species using genetically homogeneous samples

We evaluated acidification effects on two crustose coralline algal species common to Pacific coral reefs, Lithophyllum kotschyanum and Hydrolithon samoense. We used genetically homogeneous samples of both species to eliminate misidentification of species. The growth rates and percent calcification of the walls of the epithallial cells (thallus surface cells) of both species decreased with increasing pCO2. However, elevated pCO2 more strongly inhibited the growth of L. kotschyanum versus H. samoense. The trend of decreasing percent calcification of the cell wall did not differ between these species, although intercellular calcification of the epithallial cells in L. kotschyanum was apparently reduced at elevated pCO2, a result that might indicate that there are differences in the solubility or density of the calcite skeletons of these two species. These results can provide knowledge fundamental to future studies of the physiological and genetic mechanisms that underlie the response of crustose coralline algae to environmental stresses.

Differential response of two Mediterranean cold-water coral species to ocean acidification

Cold-water coral (CWC) reefs constitute one of the most complex deep-sea habitats harboring a vast diversity of associated species. Like other tropical or temperate framework builders, these systems are facing an uncertain future due to several threats, such as global warming and ocean acidification. In the case of Mediterranean CWC communities, the effect may be exacerbated due to the greater capacity of these waters to absorb atmospheric CO2 compared to the global ocean. Calcification in these organisms is an energy-demanding process, and it is expected that energy requirements will be greater as seawater pH and the availability of carbonate ions decrease. Therefore, studies assessing the effect of a pH decrease in skeletal growth, and metabolic balance are critical to fully understand the potential responses of these organisms under a changing scenario. In this context, the present work aims to investigate the medium- to long-term effect of a low pH scenario on calcification and the biochemical composition of two CWCs from the Mediterranean, Dendrophyllia cornigera and Desmophyllum dianthus. After 314 d of exposure to acidified conditions, a significant decrease of 70 % was observed in Desmophyllum dianthus skeletal growth rate, while Dendrophyllia cornigera showed no differences between treatments. Instead, only subtle differences between treatments were observed in the organic matter amount, lipid content, skeletal microdensity, or porosity in both species, although due to the high variability of the results, these differences were not statistically significant. Our results also confirmed a heterogeneous effect of low pH on the skeletal growth rate of the organisms depending on their initial weight, suggesting that those specimens with high calcification rates may be the most susceptible to the negative effects of acidification.

Responses of three tropical seagrass species to CO2 enrichment

Increased atmospheric carbon dioxide leads to ocean acidification and carbon dioxide (CO2) enrichment of seawater. Given the important ecological functions of seagrass meadows, understanding their responses to CO2 will be critical for the management of coastal ecosystems. This study examined the physiological responses of three tropical seagrasses to a range of seawater pCO2 levels in a laboratory. Cymodocea serrulata, Halodule uninervis and Thalassia hemprichii were exposed to four different pCO2 treatments (442-1204 µatm) for 2 weeks, approximating the range of end-of-century emission scenarios. Photosynthetic responses were quantified using optode-based oxygen flux measurements. Across all three species, net productivity and energetic surplus (PG:R) significantly increased with a rise in pCO2 (linear models, P < 0.05). Photosynthesis-irradiance curve-derived photosynthetic parameters-maximum photosynthetic rates (P max) and efficiency (alpha) also increased as pCO2 increased (linear models, P < 0.05). The response for productivity measures was similar across species, i.e. similar slopes in linear models. A decrease in compensation light requirement (Ec) with increasing pCO2 was evident in C. serrulata and H. uninervis, but not in T. hemprichii. Despite higher productivity with pCO2 enrichment, leaf growth rates in C. serrulata did not increase, while those in H. uninervis and T. hemprichii significantly increased with increasing pCO2 levels. While seagrasses can be carbon-limited and productivity can respond positively to CO2 enrichment, varying carbon allocation strategies amongst species suggest differential growth response between species. Thus, future increase in seawater CO2 concentration may lead to an overall increase in seagrass biomass and productivity, as well as community changes in seagrass meadows.

Seawater carbonate chemistry and calcification of two mediterranean cold-water coral species in a laboratory experiment

Deep-water ecosystems are characterized by relatively low carbonate concentration values and, due to ocean acidification (OA), these habitats might be among the first to be exposed to undersaturated conditions in the forthcoming years. However, until now, very few studies have been conducted to test how cold-water coral (CWC) species react to such changes in the seawater chemistry. The present work aims to investigate the mid-term effect of decreased pH on calcification of the two branching CWC species most widely distributed in the Mediterranean, Lophelia pertusa and Madrepora oculata. No significant effects were observed in the skeletal growth rate, microdensity and porosity of both species after 6 months of exposure. However, while the calcification rate of M. oculata was similar for all colony fragments, a heterogeneous skeletal growth pattern was observed in L. pertusa, the younger nubbins showing higher growth rates than the older ones. A higher energy demand is expected in these young, fast-growing fragments and, therefore, a reduction in calcification might be noticed earlier during long-term exposure to acidified conditions.

DAEDALUS at ImageCLEF 2011 Plant Identification Task: Using SIFT Keypoints for Object Detection

This paper describes the participation of DAEDALUS at ImageCLEF 2011 Plant Identification task. The task is evaluated as a supervised classification problem over 71 tree species from the French Mediterranean area used as class labels, based on visual content from scan, scan-like and natural photo images. Our approach to this task is to build a classifier based on the detection of keypoints from the images extracted using Lowe’s Scale Invariant Feature Transform (SIFT) algorithm. Although our overall classification score is very low as compared to other participant groups, the main conclusion that can be drawn is that SIFT keypoints seem to work significantly better for photos than for the other image types, so our approach may be a feasible strategy for the classification of this kind of visual content.

Icosahedral Ni nanowires formed from nanocontacts breaking: Identification and characterization by Molecular Dynamics

We present and discuss an algorithm to identify and characterize the long icosahedral structures (staggered pentagonal nanowires with 1-5-1-5 atomic structure) that appear in Molecular Dynamics simulations of metallic nanowires of different species subjected to stretching. The use of this algorithm allows the identification of pentagonal rings forming the icosahedral structure as well as the determination of its number np , and the maximum length of the pentagonal nanowire Lpm. The algorithm is tested with some ideal structures to show its ability to discriminate between pentagonal rings and other ring structures. We applied the algorithm to Ni nanowires with temperatures ranging between 4K and 865K, stretched along the [111], [100] and [110] directions. We studied statistically the formation of pentagonal nanowires obtaining the distributions of length Lpm and number of rings np as function of the temperature. The Lpm distribution presents a peaked shape, with peaks located at fixed distances whose separation corresponds to the distance between two consecutive pentagonal rings.

A new method for the identification of old-growth trees in National Forest Inventories: Application to Pinus halepensis Mill. stands in Spain

Old-growth trees play a very important role in the maintenance of biodiversity in forests. However, no clear definition is yet available to help identify them since tree age is usually not recorded in National Forest Inventories. To develop and test a new method to identify old-growth trees using a species-specific threshold for tree diameter in National Forest Inventories. Different nonlinear mixed models for diameter ? age were generated using data from the Spanish Forest Inventory in order to identify the most appropriate one for Aleppo pine in its South-western distribution area. The asymptote of the optimal model indicates the threshold diameter for defining an old-growth tree. Additionally, five site index curves were examined to analyze the influence of site quality on these models.

Identification and analysis of a nickel-inducible cation diffusion facilitator-NiCoT combined system in Rhizobium leguminosarum bv. viciae

Nickel, like other transition metals, can be toxic to cells even at moderate concentration (low microM range) by displacing essential metals from their native binding sites or by generating reactive oxygen species that cause oxidative DNA damage. For this reason, cells have evolved mechanisms to deal with excess nickel. Efflux systems include members of the Resistance-Nodulation-cell Division (RND) protein family, P-type ATPases, cation diffusion facilitators (CDF) and other resistance factors. Nickel-specific exporters have been characterized in Cupravidus metallidurans, Helicobacter pylori, Achromobacter xylosoxidans, Serratia marcenses and Escherichia coli.

A taxonomic tool for identifying needle remains of south-western European Pinus species of the Late Quaternary

This work provides a tool whereby the needle remains of native, south-western European Pinus spp. can be easily identified from species-specific epidermal features. To construct this tool, the needles of P. uncinata, P. sylvestris, P. nigra, P. pinaster, P. pinea and P. halepensis were gathered across the Northern Hemisphere range of each taxon and compared with non-indigenous trees growing in two South Australian Botanic Gardens. Three needles from each of these species were taken from three adult trees growing at three different localities. Light microscopy was used to observe the key epidermal and stomatal features of the needles. To improve interpretation, additional scanning electron microscopy samples were prepared. Epidermal features, including variation in the diameter of the epistomatal chamber aperture (pore), are described. A taxonomic key based on the size, shape and arrangement of the subsidiary cells of the stomatal complexes was constructed. This key enables the identification of pine needle fragments at the species level (except those belonging to the group P. gr. nigra-uncinata). Despite their overlapping range, pore size was helpful in distinguishing between P. nigra and P. uncinata and between three groups of species. Isolated stomata were also observed. Cluster and discriminant analyses of stomatal variables described in earlier studies were performed. Overlap in guard cell variables hampers species-level identification of isolated stomata. Species discrimination is improved if groups of ecological affinity are considered.