Antarctic DNA barcoding; a drop in the ocean?

Coordinated, circum-Antarctic sampling expeditions during International Polar Year 2008/09 have given access to comprehensive collections suitable for DNA barcoding. Collaborations between the Census of Antarctic Marine Life (CAML), the Marine Barcode of Life project and the Canadian Centre for DNA Barcoding have enabled the Antarctic scientific community to initiate large-scale DNA barcoding projects to record the genetic diversity of Antarctic marine fauna, coordinated by the CAML Barcoding Campaign. A total of 20,355 marine specimens from more than 2,000 morphospecies covering 18 phyla are in the processing pipeline, and to date, 11,530 sequences have been processed with the remainder due by the end of 2010. Here, we present results on the current geographic and taxonomic coverage of DNA barcode data in the Southern Ocean and identify the remaining gaps. We show how DNA barcoding in the Antarctic is answering important questions regarding marine genetic diversity and challenging current assumptions of species distribution at the poles.     

Do enzymes bind their substrates in the ground state because of a physico-chemical requirement?

Transition state theory has provided no convincing explanation for the nearly universal observation of complexes of enzymes with substrates. Bimolecular catalytic reactions are assumed here to take place through reactive encounter complexes defined as the subset of reactant state species able to proceed directly to low lying energy levels at the transition state. By assessing the probability of these complexes from the maximum efficiency of intramolecular reactions, an upper limit for the rate constants promoted by hypothetical catalysts unable to bind substrates is deduced. This limit, which is below the ordinary range of bimolecular rate constants (k(cat)/K(M)) for enzyme reactions, results from a kinetic limitation in the formation of reactive encounter complexes. Exceeding this limit requires a stabilization of these complexes. Using the terminology of transition state theory, the need for enzymes to form complexes with substrates is then expressed as a necessity to restore Boltzmann distribution at the transition state.     

Do calanoid copepods suppress appendicularians in the coastal ocean?

In a mesocosm study, the appendicularian Oikopleura dioica bloomedafter the reduction of copepod abundance, and in a second treatmentshowed a significantly negative correlation with copepod densities.Calculations, together with field data from the Baltic Sea,suggest that common calanoid copepods may control appendicularianpopulation dynamics.     

Invariant glycines and prolines flanking in loops the strand beta 2 of various (alpha/beta)8-barrel enzymes: a hidden homology?

The question of parallel (alpha/beta)8-barrel fold evolution remains unclear, owing mainly to the lack of sequence homology throughout the amino acid sequences of (alpha/beta)8-barrel enzymes. The "classical" approaches used in the search for homologies among (alpha/beta)8-barrels (e.g., production of structurally based alignments) have yielded alignments perfect from the structural point of view, but the approaches have been unable to reveal the homologies. These are proposed to be "hidden" in (alpha/beta)8-barrel enzymes. The term "hidden homology" means that the alignment of sequence stretches proposed to be homologous need not be structurally fully satisfactory. This is due to the very long evolutionary history of all (alpha/beta)8-barrels. This work identifies so-called hidden homology around the strand beta 2 that is flanked by loops containing invariant glycines and prolines in 17 different (alpha/beta)8-barrel enzymes, i.e., roughly in half of all currently known (alpha/beta)8-barrel proteins. The search was based on the idea that a conserved sequence region of an (alpha/beta)8-barrel enzyme should be more or less conserved also in the equivalent part of the structure of the other enzymes with this folding motif, given their mutual evolutionary relatedness. For this purpose, the sequence region around the well-conserved second beta-strand of alpha-amylase flanked by the invariant glycine and proline (56_GFTAIWITP, Aspergillus oryzae alpha-amylase numbering), was used as the sequence-structural template. The proposal that the second beta-strand of (alpha/beta)8-barrel fold is important from the evolutionary point of view is strongly supported by the increasing trend of the observed beta 2-strand structural similarity for the pairs of (alpha/beta)8-barrel enzymes: alpha-amylase and the alpha-subunit of tryptophan synthase, alpha-amylase and mandelate racemase, and alpha-amylase and cyclodextrin glycosyltransferase. This trend is also in agreement with the existing evolutionary division of the entire family of (alpha/beta)8-barrel proteins.     

Sex in the PAC: A hidden affair in dark septate endophytes?

Background

Fungi are asexually and sexually reproducing organisms that can combine the evolutionary advantages of the two reproductive modes. However, for many fungi the sexual cycle has never been observed in the field or in vitro and it remains unclear whether sexual reproduction is absent or cryptic. Nevertheless, there are indirect approaches to assess the occurrence of sex in a species, such as population studies, expression analysis of genes involved in mating processes and analysis of their selective constraints. The members of the Phialocephala fortinii s. l. - Acephala applanata species complex (PAC) are ascomycetes and the predominant dark septate endophytes that colonize woody plant roots. Despite their abundance in many ecosystems of the northern hemisphere, no sexual state has been identified to date and little is known about their reproductive biology, and how it shaped their evolutionary history and contributes to their ecological role in forest ecosystems. We therefore aimed at assessing the importance of sexual reproduction by indirect approaches that included molecular analyses of the mating type (MAT) genes involved in reproductive processes.

Results

The study included 19 PAC species and > 3, 000 strains that represented populations from different hosts, continents and ecosystems. Whereas A. applanata had a homothallic (self-fertile) MAT locus structure, all other species were structurally heterothallic (self-sterile). Compatible mating types were observed to co-occur more frequently than expected by chance. Moreover, in > 80% of the populations a 1:1 mating type ratio and gametic equilibrium were found. MAT genes were shown to evolve under strong purifying selection.

Conclusions

The signature of sex was found in worldwide populations of PAC species and functionality of MAT genes is likely preserved by purifying selection. We hypothesize that cryptic sex regularely occurs in the PAC and that further field studies and in vitro crosses will lead to the discovery of the sexual state. Although structurally heterothallic species prevail, it cannot be excluded that homothallism represents the ancestral breeding system in the PAC.     

Are white-rot fungi a real biotechnological option for the improvement of environmental health?

The use of white-rot fungi as a biotechnological tool for cleaning the environment of recalcitrant pollutants has been under evaluation for several years. However, it is still not possible to find sufficiently detailed investigations of this subject to conclude that these fungi can decontaminate the environment. In the present review, we have summarized and discussed evidence about the potential of white-rot fungi to degrade such pollutants as polycyclic aromatic hydrocarbons, dyes or antibiotics as an example of the complex structures that these microorganisms can attack. This review also discusses field experiment results and limitations of white-rot fungi trials from contaminated sites. Moreover, the use of catabolic potential of white-rot fungi in biopurification systems (biobeds) is also discussed. The current status and future perspectives of white-rot fungi, as a viable biotechnological alternative for improvement of environmental health are noted.     

Do the extracellular enzymes cellobiose dehydrogenase and manganese peroxidase form a pathway in lignin biodegradation?

The extracellular enzyme manganese peroxidase is believed to degrade lignin by a hydrogen peroxide-dependent oxidation of Mn(II) to the reactive species Mn(III) that attacks the lignin. However, Mn(III) is not able to directly oxidise the non-phenolic lignin structures that predominate in native lignin. We show here that pretreatment of a non-phenolic lignin model compound with another extracellular fungal enzyme, cellobiose dehydrogenase, allows the manganese peroxidase system to oxidise this molecule. The mechanism behind this effect is demethoxylation and/or hydroxylation, i.e. conversion of a non-phenolic structure to a phenolic one, mediated by hydroxyl radicals generated by cellobiose dehydrogenase. This suggests that cellobiose dehydrogenase and manganese peroxidase may act in an extracellular pathway in fungal lignin biodegradation. Analytical techniques used in this paper are reverse-phase high-pressure liquid chromatography, gas chromatography connected to mass spectroscopy and UV-visible spectroscopy.     

What is the Fungal Diversity of Marine Ecosystems in Europe?

In 2001 the European Register of Marine Species 1.0 was published (Costello et al. 2001 and http://erms.biol.soton.ac.uk/, and latterly: http://www.marbef.org/data/stats.php) [Costello MJ, Emblow C, White R, 2001. European register of marine species: a check list of the marine species in Europe and a bibliography of guides to their identification. Collection Patrimoines Naturels50, 463p.]. The lists of species (from fungi to mammals) were published as part of a European Union Concerted action project (funded by the European Union Marine Science and Technology (MAST) research programme) and the updated version (ERMS 2) is EU-funded through the Marine Biodiversity and Ecosystem Functioning (MARBEF) Framework project 6 Network of Excellence. Among these lists, a list of the fungi isolated and identified from coastal and marine ecosystems in Europe was included (Clipson et al. 2001) [Clipson NJW, Landy ET, Otte ML, 2001. Fungi. In@ Costelloe MJ, Emblow C, White R (eds), European register of marine species: a check-list of the marine species in Europe and a bibliography of guides to their identification. Collection Patrimoines Naturels50: 15-19.]. This article deals with the results of compiling a new taxonomically correct and complete list of all fungi that have been reported occurring in European marine waters.     

Marine metapopulations: a useful concept?

We discuss the potential and limitations of the metapopulation concept in marine ecology. The usefulness of the concept in terrestrial ecology is neither based on its simplicity or generality nor on overwhelming empirical evidence. The usefulness is in the questions which are asked when the metapopulation concept is applied. These questions address spatial phenomena and processes on different spatial scales. They help in acknowledging that every population, be it terrestrial or marine, has a spatial organization. Understanding this spatial organization is also important for tackling specific applied problems, i.e. to avoid overexploitation of living marine resources or for configuring marine reserves. The 'openness' of coastal populations, whose larvae enter larval pools or which are holoplanktonic, is no reason for not asking the questions implied by the metapopulation concept. For marine ecology, the real problem is to delineate populations, which then may possibly correspond to the 'local populations' of metapopulations. Thus, the answer to the question in the title of this paper, whether 'marine metapopulation' is a useful concept, is 'yes', if the concept is considered a working hypotheses, if the concept is explicitly defined, and if the questions linked to the concept are clearly stated. Even if it eventually transpires that only very few marine metapopulations actually exist, marine ecology would still have gained some important new insights. Electronic Publication     

ROS,autophagy, mitochondria and cancer: Ras,the hidden master?

Recent advances have highlighted the complex web of biological mechanisms and pathways involved in oncogenic transformation and maintenance of the cancer phenotype. To that end, a number of key factors have been identified and thoroughly investigated over the past couple of decades, such as redox regulation of cell fate decisions, cellular metabolism and bioenergetics, autophagy induction as a survival signal, and how these pathways interplay with oncogene-induced transformation. This has been particularly well documented for oncoprotein Ras-induced carcinogenesis, and recent reports provide ample evidence to indicate a well-coordinated crosstalk between these diverse cellular pathways in the process of cancer initiation and progression. Here we provide a brief summary of the recent advances in the field to illustrate the dual role of autophagy as a tumor suppressor and as a survival mechanism required for cancer maintenance as well as its implication in the complex relationship between Ras-mediated carcinogenesis, mitochondrial metabolism, cellular redox status and bioenergetics.     

Calcium, a signaling molecule in the endoplasmic reticulum?

For many years now, it has been known that Ca2+ is an important signaling molecule in the cytosol of the cell, but emerging evidence suggests that Ca2+ might also play a signaling role in the endoplasmic reticulum. For example, agonist-induced fluctuations in free Ca2+ concentration in the endoplasmic reticulum can affect many functions of the endoplasmic reticulum, including protein synthesis and modification, and interchaperone interactions.     

Protecting or Pilfering? Neoliberal Conservationist Marine Protected Areas in the Experience of Coastal Granada,the Philippines

In recent years conservationist NGOs, policy makers, and scientists in the tropics have expressed a fascination with marine protected areas for simultaneously achieving conservation goals and economic development. Despite their popularity, MPAs often encounter serious implementation challenges due to, at least to some extent, our limited understanding of MPA processes as influenced by neoliberal ideology and practice. By resituating MPAs in debates of neoliberal conservation, this study aims to examine social and economic changes that MPAs bring about in fishing communities. Taking a fishing village in the Philippines as a case study, it shows technocratic solution seeking led to further marginalization of small-scale fishers through unequal distribution of benefits and burdens. Here it is argued that MPAs are prone to exclusionist processes of redefining the value and legitimate users of marine resources, which further limits the opportunities for small-scale fishers to participate meaningfully in resource governance.     

Not berry hungry? Discovering the hidden food sources of a small fruit specialist,Drosophila suzukii

1. Although polyphagy is widespread among Drosophila, some specialist species have evolved in response to resource competition and other selection factors favouring niche separation. The small fruit specialist Drosophila suzukii Matsumura has evolved a unique serrated ovipositor that allows it to access ripening fruit, a niche unavailable to most Drosophila. However, it is unclear whether ancestral traits (the use of non‐fruit resources) are maintained in this specialist species. 2. In this study, maternal preferences and offspring fitness in response to novel apple, mushroom, and bird manure‐based diets were investigated by comparing oviposition and offspring survival and development on various diets. The effect of those diets on survival at cool temperatures and the effect of natal environment/previous exposure on adult preferences were evaluated. 3. Female D. suzukii accepted non‐fruit diets such as mushroom and bird manure, and offspring completed their larval development on all diets tested. However, D. suzukii did not perform well on diets that included bird manure. By contrast, combinational apple/mushroom diets were associated with greater oviposition, lower mortality, faster development, and larger offspring than other diets. These diets were also associated with increased resistance to cold stress, and preference for these diets was positively affected by previous feeding experience. 4. These data suggest that D. suzukii may use non‐fruit resources when preferred resources are scarce. Given that this pest is adapted to temperate climates, alternative resources might provide seasonal nutritional support when fruit resources are not temporally available, although field data are needed to support this hypothesis.     

Have we been underestimating the effects of ocean acidification in zooplankton?

Understanding how copepods may respond to ocean acidification (OA) is critical for risk assessments of ocean ecology and biogeochemistry. The perception that copepods are insensitive to OA is largely based on experiments with adult females. Their apparent resilience to increased carbon dioxide (pCO₂) concentrations has supported the view that copepods are ‘winners’ under OA. Here, we show that this conclusion is not robust, that sensitivity across different life stages is significantly misrepresented by studies solely using adult females. Stage‐specific responses to pCO₂ (385–6000 μatm) were studied across different life stages of a calanoid copepod, monitoring for lethal and sublethal responses. Mortality rates varied significantly across the different life stages, with nauplii showing the highest lethal effects; nauplii mortality rates increased threefold when pCO₂ concentrations reached 1000 μatm (year 2100 scenario) with LC₅₀ at 1084 μatm pCO₂. In comparison, eggs, early copepodite stages, and adult males and females were not affected lethally until pCO₂ concentrations ≥3000 μatm. Adverse effects on reproduction were found, with >35% decline in nauplii recruitment at 1000 μatm pCO₂. This suppression of reproductive scope, coupled with the decreased survival of early stage progeny at this pCO₂ concentration, has clear potential to damage population growth dynamics in this species. The disparity in responses seen across the different developmental stages emphasizes the need for a holistic life‐cycle approach to make species‐level projections to climate change. Significant misrepresentation and error propagation can develop from studies which attempt to project outcomes to future OA conditions solely based on single life history stage exposures.     

Regulation of the oxidative stress protective enzymes,catalase and superoxide dismutase in Xanthomonas — a review

Xanthomonas showed atypical regulation of catalase (Kat) and superoxide dismutase with respect to growth phase and response to various inducers. The highest levels of both enzymes were detected during early log phase of growth and declined as growth continued. This was in contrast to resistance levels to superoxides, H₂O₂ and organic peroxides, which reached maximum levels during stationary phase. Xanthomonas catalase was induced over six fold by superoxide generators and methyl methane sulfonate but weakly by H₂O₂. The regulation pattern of these enzymes could be important during plant/microbe interactions. To facilitate elucidation of Xanthomonas kat gene regulation, highly conserved regions of monofuctional Kat amino acid sequences were used to synthesize oligodeoxyribonucleotide primers for use in PCR reactions with Xanthomonas genomic DNA as templates. The Xanthomonas-specific PCR kat probe was used to isolate a functional kat from Xanthomonas campestris pv. phaseoli.     

Do phospholipases, key enzymes in sperm physiology, represent therapeutic challenges?

The spermatozoon is one of the most differentiated cells in mammals and its production requires an extremely complex machinery. Subtle but critical molecular changes take place during capacitation, which comprises the last series of maturation steps that naturally occur between the cauda epididymidis where spermatozoa are stored and their ultimate destination inside the oocyte. Phospholipases, by hydrolyzing various phospholipids, have been found to be critical in sperm processes such as 1) the control of flagellum beats, 2) capacitation - the molecular transformations preparing the sperm for fertilization, 3) acrosome reaction and 4) oocyte activation by eliciting calcium oscillations. The emerging important role of phospholipases is also emphasized by the fact that alterations of sperm lipids can lead to infertility. Phospholipases may represent valuable targets to develop anti- and pro-fertility drugs. Results obtained in mice are encouraging, since treatment of sperm with recombinant sPLA(2) of group X, known to be involved in capacitation, improves fertilization in vitro, while co-injection of PLCζ RNA with infertile sperm restores oocyte activation.     

Principles of Biofouling Protection in Marine Sponges: A Model for the Design of Novel Biomimetic and Bio-inspired Coatings in the Marine Environment?

The process of biofouling of marine structures and substrates, such as platforms or ship hulls, proceeds in multiple steps. Soon after the formation of an initial conditioning film, formed via the adsorption of organic particles to natural or man-made substrates, a population of different bacterial taxa associates under the formation of a biofilm. These microorganisms communicate through a complex quorum sensing network. Macro-foulers, e.g., barnacles, then settle and form a fouling layer on the marine surfaces, a process that globally has severe impacts both on the economy and on the environment. Since the ban of tributyltin, an efficient replacement of this antifouling compound by next-generation antifouling coatings that are environmentally more acceptable and also showing longer half-lives has not yet been developed. The sponges, as sessile filter-feeder animals, have evolved antifouling strategies to protect themselves against micro- and subsequent macro-biofouling processes. Experimental data are summarized and suggest that coating of the sponge surface with bio-silica contributes to the inhibition of the formation of a conditioning film. A direct adsorption of the surfaces by microorganisms can be impaired through poisoning the organisms with direct-acting secondary metabolites or toxic peptides. In addition, first, compounds from sponges have been identified that interfere with the anti-quorum sensing network. Sponge secondary metabolites acting selectively on diatom colonization have not yet been identified. Finally, it is outlined that direct-acting secondary metabolites inhibiting the growth of macro-fouling animals and those that poison the multidrug resistance pump are available. It is concluded that rational screening programs for inhibitors of the complex and dynamic problem of biofilm production, based on multidisciplinary studies and using sponges as a model, are required in the future.