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As the role of mercury is poorly known in Southern Ocean biota, the total mercury (T-Hg) concentrations were evaluated in upper/lower beaks, digestive gland, gills and mantle muscle of Adelieledone polymorpha and Pareledone turqueti, two of the most abundant octopod species around South Georgia. Beaks had the lowest T-Hg concentrations (A. polymorpha: [T-Hg] Upper  = 27.2 ± 12.9 ng∙g -1 and [T-Hg] Lower  = 27.5 ± 20.0 ng∙g -1 ; P. turqueti: [T-Hg] Upper  = 34.6 ± 13.9 ng∙g -1 and [T-Hg] Lower  = 56.8 ± 42.0 ng∙g -1 ), followed by gills and muscle. The highest values were recorded in the digestive gland (A. polymorpha: 251.6 ± 69.7 ng∙g -1 ; P. turqueti: 347.0 ± 177.0 ng∙g -1 ). Significant relationships were found between the concentrations of T-Hg in the beaks and muscle of A. polymorpha (T-Hg in muscle is 10 times higher than in beaks). This study shows that beaks can be used as proxy for T-Hg in muscle for some octopod species, and a helpful tool for estimating total Hg body burden from beaks., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Myctophids are the most abundant fish group in the Southern Ocean pelagic ecosystem and are an important link in the Antarctic marine food web. Due to their major ecological role, evaluating the level of mercury (Hg) contamination in myctophids is important as a step towards understanding the trophic pathway of this contaminant. The concentrations of total Hg were determined in muscle, gill, heart and liver tissue of 9 myctophid species to quantify tissue partitioning variability between species. Organic Hg concentration and proportion in muscle was also determined. Hg concentrations were higher in the liver and heart than in muscle and gills, but the proportion of organic Hg was almost 100% in muscle, indicating that the main uptake route for Hg is through the diet. Most of the species analysed have similar vertical and horizontal distributions, and similar feeding modes and prey. Geographical and temporal variability of Hg concentrations was examined using samples from 3 different sampling cruise (2007/08, 2015/16 and 2016/17) and 2 locations (South Georgia and South Orkneys Islands). Our results appear to indicate a decreasing trend in Hg contamination over the last decade, particularly gill tissue, which is in agreement with a previous study on squid from the same region. There was no significant variability in Hg concentration between the different sampling locations. Hg levels were consistent with values reported previously for myctophids around the world, indicating low global-scale geographic variability. A positive relationship between fish size and Hg concentration was found for most species, with the exception of Electrona antarctica females, which may be explained through Hg elimination by egg laying. We estimate that myctophids collectively comprise a Southern Ocean mercury 'reserve' of ≈1.82 metric tonnes., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Mercury is a bioaccumulating toxic pollutant which can reach humans through the consumption of contaminated food (e.g. marine fish). Although the Southern Ocean is often portrayed as a pristine ecosystem, its fishery products are not immune to mercury contamination. We analysed mercury concentration (organic and inorganic forms - T-Hg) in the muscle of Antarctic toothfish, Dissostichus mawsoni, a long-lived top predator which supports a highly profitable fishery. Our samples were collected in three fishing areas (one seamount and two on the continental slope) in the Southwest Pacific Sector of the Southern Ocean during the 2016/2017 fishing season. Mercury levels and the size range of fish varied between fishing areas, with the highest levels (0.68 ± 0.45 mg kg -1 wwt) occurring on the Amundsen Sea seamount where catches were dominated by larger, older fish. The most parsimonious model of mercury concentration included both age and habitat (seamount vs continental slope) as explanatory variables. Mean mercury levels for each fishing area were higher than those in all previous studies of D. mawsoni, with mean values for the Amundsen Sea seamount exceeding the 0.5 mg kg -1 food safety threshold for the first time. It might therefore be appropriate to add D. mawsoni to the list of taxa, such as swordfish and sharks, which are known to exceed this threshold. This apparent increase in mercury levels suggests a recent contamination event which affected the Southwest Pacific sector, including both the Amundsen and Dumont D'Urville seas., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier Inc. All rights reserved.)

Background: To analyze biochemical and microbiological parameters of the saliva of institutionalized elders and to investigate the relation of these parameters with edentulism, use of dentures and presence of biofilm., Material and Methods: A cross-sectional study carried was out in seven long-term institutions. Samples (n=161) of unstimulated saliva were collected for analysis of salivary flow, quantification of total proteins and identification of microorganisms. Oral examination was carried out to verify the number of missing teeth, the use of dentures and the presence of visible biofilm on the surface of teeth and dentures. Associations were performed using chi-square or Fisher's exact test (α<0.05). Mann-Whitney Test was used to identify differences in the salivary flow and total proteins (α<0.05)., Results: There was no association between the type of edentulism and use of dentures with biochemical and microbiological parameters of saliva ( p >0.05). Associations were observed between the presence of dentures biofilm and the colonization of Streptococcus sp. ( p =0.038) and Candida sp. ( p =0.03)., Conclusions: The absence of teeth and use of dentures do not influence the amount of total proteins and the microorganisms count in saliva. Denture biofilms are associated with the presence of Streptococcus sp. and Candida sp. in saliva of institutionalized elders. Key words: Candida, long-stay institutions for elders, saliva, Streptococcus, Staphylococcus., Competing Interests: Conflicts of interest There was no conflict of interests in this study., (Copyright: © 2020 Medicina Oral S.L.)

Southern Ocean ecosystems are under pressure from resource exploitation and climate change 1,2 . Mitigation requires the identification and protection of Areas of Ecological Significance (AESs), which have so far not been determined at the ocean-basin scale. Here, using assemblage-level tracking of marine predators, we identify AESs for this globally important region and assess current threats and protection levels. Integration of more than 4,000 tracks from 17 bird and mammal species reveals AESs around sub-Antarctic islands in the Atlantic and Indian Oceans and over the Antarctic continental shelf. Fishing pressure is disproportionately concentrated inside AESs, and climate change over the next century is predicted to impose pressure on these areas, particularly around the Antarctic continent. At present, 7.1% of the ocean south of 40°S is under formal protection, including 29% of the total AESs. The establishment and regular revision of networks of protection that encompass AESs are needed to provide long-term mitigation of growing pressures on Southern Ocean ecosystems.

The Retrospective Analysis of Antarctic Tracking Data (RAATD) is a Scientific Committee for Antarctic Research project led jointly by the Expert Groups on Birds and Marine Mammals and Antarctic Biodiversity Informatics, and endorsed by the Commission for the Conservation of Antarctic Marine Living Resources. RAATD consolidated tracking data for multiple species of Antarctic meso- and top-predators to identify Areas of Ecological Significance. These datasets and accompanying syntheses provide a greater understanding of fundamental ecosystem processes in the Southern Ocean, support modelling of predator distributions under future climate scenarios and create inputs that can be incorporated into decision making processes by management authorities. In this data paper, we present the compiled tracking data from research groups that have worked in the Antarctic since the 1990s. The data are publicly available through biodiversity.aq and the Ocean Biogeographic Information System. The archive includes tracking data from over 70 contributors across 12 national Antarctic programs, and includes data from 17 predator species, 4060 individual animals, and over 2.9 million observed locations.

Modern cells embody metabolic networks containing thousands of elements and form autocatalytic sets of molecules that produce copies of themselves. How the first self-sustaining metabolic networks arose at life's origin is a major open question. Autocatalytic sets smaller than metabolic networks were proposed as transitory intermediates at the origin of life, but evidence for their role in prebiotic evolution is lacking. Here, we identify reflexively autocatalytic food-generated networks (RAFs)-self-sustaining networks that collectively catalyse all their reactions-embedded within microbial metabolism. RAFs in the metabolism of ancient anaerobic autotrophs that live from H 2 and CO 2 provided with small-molecule catalysts generate acetyl-CoA as well as amino acids and bases, the monomeric components of protein and RNA, but amino acids and bases without organic catalysts do not generate metabolic RAFs. This suggests that RAFs identify attributes of biochemical origins conserved in metabolic networks. RAFs are consistent with an autotrophic origin of metabolism and furthermore indicate that autocatalytic chemical networks preceded proteins and RNA in evolution. RAFs uncover intermediate stages in the emergence of metabolic networks, narrowing the gaps between early Earth chemistry and life.

Research on the origin of life is highly heterogeneous. After a peculiar historical development, it still includes strongly opposed views which potentially hinder progress. In the 1st Interdisciplinary Origin of Life Meeting, early-career researchers gathered to explore the commonalities between theories and approaches, critical divergence points, and expectations for the future. We find that even though classical approaches and theories-e.g. bottom-up and top-down, RNA world vs. metabolism-first-have been prevalent in origin of life research, they are ceasing to be mutually exclusive and they can and should feed integrating approaches. Here we focus on pressing questions and recent developments that bridge the classical disciplines and approaches, and highlight expectations for future endeavours in origin of life research.

This study examines age and growth of Brauer's lanternfish Gymnoscopelus braueri and rhombic lanternfish Krefftichthys anderssoni from the Scotia Sea in the Southern Ocean, through the analysis of annual growth increments deposited on sagittal otoliths. Otolith pairs from 177 G. braueri and 118 K. anderssoni were collected in different seasons from the region between 2004 and 2009. Otolith-edge analysis suggested a seasonal change in opaque and hyaline depositions, indicative of an annual growth pattern, although variation within the populations of both species was apparent. Age estimates varied from 1 to 6 years for G. braueri (40 to 139 mm standard length; L S ) and from 0 to 2 years for K. anderssoni (26 to 70 mm L S ). Length-at-age data were broadly consistent with population cohort parameters identified in concurrent length-frequency data from the region for both species. The estimated values of von Bertalanffy growth curves for G. braueri were L ∞ = 133.22 mm, k = 0.29 year -1 and t 0 = -0.21 year and the values for K. anderssoni were L ∞ = 68.60 mm, k = 0.71 year -1 and t 0 = -0.49 year. There were no significant (P > 0.05) differences in growth between sexes for either species, suggesting that males and females have similar growth and development trajectories in the Scotia Sea. A positive allometric relationship between L S and wet mass was found for each species, as well as a significant (P < 0.0001) linear relationship between otolith size and L S . Growth performance (Ф') was similar between the two species and congruent with other myctophid species across the Southern Ocean. This study provides important parameters for future Southern Ocean ecosystem studies in a resource management context., (© 2019 The Fisheries Society of the British Isles.)

The concentrations of total and proportions of organic mercury were measured in tissues of 355 individuals of 8 species of Southern Ocean squid (Alluroteuthis antarcticus, Bathyteuthis abyssicola, Filippovia knipovitchi, Galiteuthis glacialis, Gonatus antarcticus, Kondakovia longimana, Psychroteuthis glacialis and Slosarczykovia circumantarctica). Squid were caught around South Georgia (Scotia Sea) during 5 cruises, between the austral summers of 2006/07 to 2016/17 to evaluate temporal changes in bioaccumulation and tissue partitioning. Total mercury concentrations varied between 4 ng g -1 and 804 ng g -1 among all tissues. Net accumulation of mercury in muscle with size was observed in A. antarcticus, B. abyssicola and P. glacialis, but no relationship was found for S. circumantarctica and lower concentrations were observed in larger individuals of G. glacialis. Muscle tissues had the highest mercury concentrations in the majority of species, except for F. knipovitchi for which the digestive gland contained highest concentrations. In terms of the percentage of organic mercury in the tissues, muscle always contained the highest values (67%-97%), followed by the digestive gland (22%-38%). Lowest organic mercury percentages were found consistently in the gills (9%-19%), suggesting only low levels of incorporation through the dissolved pathway and/or a limited redistribution of dietary organic mercury towards this tissue. Overall, results are indicative of a decreasing trend of mercury concentrations in the majority of analysed species over the last decade. As cephalopods are an important Southern Ocean trophic link between primary consumers and top predators, these changes suggest decreasing mercury levels in lower trophic levels and an alleviation of the mercury burden on higher predators that consume squid., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Vampyroteuthis infernalis Chun, 1903, is a widely distributed deepwater cephalopod with unique morphology and phylogenetic position. We assessed its habitat and trophic ecology on a global scale via stable isotope analyses of a unique collection of beaks from 104 specimens from the Atlantic, Pacific and Indian Oceans. Cephalopods typically are active predators occupying a high trophic level (TL) and exhibit an ontogenetic increase in δ 15 N and TL. Our results, presenting the first global comparison for a deep-sea invertebrate, demonstrate that V. infernalis has an ontogenetic decrease in δ 15 N and TL, coupled with niche broadening. Juveniles are mobile zooplanktivores, while larger Vampyroteuthis are slow-swimming opportunistic consumers and ingest particulate organic matter. Vampyroteuthis infernalis occupies the same TL (3.0-4.3) over its global range and has a unique niche in deep-sea ecosystems. These traits have enabled the success and abundance of this relict species inhabiting the largest ecological realm on the planet.

If life on Earth started out in geochemical environments like hydrothermal vents, then it started out from gasses like CO 2 , N 2 and H 2 . Anaerobic autotrophs still live from these gasses today, and they still inhabit the Earth's crust. In the search for connections between abiotic processes in ancient geological systems and biotic processes in biological systems, it becomes evident that chemical activation (catalysis) of these gasses and a constant source of energy are key. The H 2 -CO 2 redox reaction provides a constant source of energy and anabolic inputs, because the equilibrium lies on the side of reduced carbon compounds. Identifying geochemical catalysts that activate these gasses en route to nitrogenous organic compounds and small autocatalytic networks will be an important step towards understanding prebiotic chemistry that operates only on the basis of chemical energy, without input from solar radiation. So, if life arose in the dark depths of hydrothermal vents, then understanding reactions and catalysts that operate under such conditions is crucial for understanding origins., Competing Interests: We declare we have no competing interests., (© 2019 The Authors.)

There is growing evidence that microplastic pollution (<5 mm in size) is now present in virtually all marine ecosystems, even in remote areas, such as the Arctic and the Antarctic. Microplastics have been found in water and sediments of the Antarctic but little is known of their ingestion by higher predators and mechanisms of their entry into Antarctic marine food webs. The goal of this study was to assess the occurrence of microplastics in a top predator, the gentoo penguin Pygoscelis papua from the Antarctic region (Bird Island, South Georgia and Signy Island, South Orkney Islands) and hence assess the potential for microplastic transfer through Antarctic marine food webs. To achieve this, the presence of microplastics in scats (as a proof of ingestion) was investigated to assess the viability of a non-invasive approach for microplastic analyses in Antarctic penguins. A total of 80 penguin scats were collected and any microplastics they contained were extracted. A total of 20% of penguin scats from both islands contained microplastics, consisting mainly of fibers and fragments with different sizes and polymer composition (mean abundance of microplastics: 0.23 ± 0.53 items individual -1 scat, comprising seven different polymers), which were lower values than those found for seabirds in other regions worldwide. No significant differences in microplastic numbers in penguin scats between the two regions were detected. These data highlight the need for further assessment of the levels of microplastics in this sensitive region of the planet, specifically studies on temporal trends and potential effects on penguins and other organisms in the Antarctic marine food web.

Sympatry can lead to higher competition under climate change and other environmental pressures, including in South Georgia, Antarctica, where the two most common octopod species, Adelieledone polymorpha and Pareledone turqueti, occur side by side. Since cephalopods are typically elusive animals, the ecology of both species is poorly known. As beaks of cephalopods are recurrently found in top predator's stomachs, we studied the feeding ecology of both octopods through the evaluation of niche overlapping and specific beak adaptations that both species present. A multidisciplinary approach combining carbon (δ 13 C) and nitrogen (δ 15 N) stable isotope signatures, mercury (Hg) analysis and biomaterials' engineering techniques was applied to investigate the beaks. An isotopic niche overlap of 95.6% was recorded for the juvenile stages of both octopod species, dropping to 19.2% for the adult stages. Both A. polymorpha and P. turqueti inhabit benthic ecosystems around South Georgia throughout their lifecycles (δ 13 C: -19.21 ± 1.87‰, mean ± SD for both species) but explore trophic niches partially different during adult life stages (δ 15 N: 7.01 ± 0.40‰, in A. polymorpha, and 7.84 ± 0.65‰, in P. turqueti). The beaks of A. polymorpha are less dense and significantly less stiff than in P. turqueti. Beaks showed lower mercury concentration relative to muscle (A. polymorpha - beaks: 0.052 ± 0.009  μg g -1 , muscle: 0.322 ± 0.088  μg g -1 ; P. turqueti - beaks: 0.038 ± 0.009  μg g -1 ; muscle: 0.434 ± 0.128  μg g -1 ). Overall, both octopods exhibit similar habitats but different trophic niches, related to morphology/function of beaks. The high Hg concentrations in both octopods can have negative consequences on their top predators and may increase under the present climate change context., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Total and organic mercury concentrations were determined for males, females and juveniles of Euphausia superba collected at three discrete locations in the Scotia Sea (South Orkney Islands, South Georgia and Antarctic Polar Front) to assess spatial mercury variability in Antarctic krill. There was clear geographic differentiation in mercury concentrations, with specimens from the South Orkney Islands having total mercury concentrations 5 to 7 times higher than Antarctic krill from South Georgia and the Antarctic Polar Front. Mercury did not appear to accumulate with life-stage since juveniles had higher concentrations of total mercury (0.071 μg g -1 from South Orkney Islands; 0.014 μg g -1 from South Georgia) than adults (0.054 μg g -1 in females and 0.048 μg g -1 in males from South Orkney Islands; 0.006 μg g -1 in females and 0.007 μg g -1 in males from South Georgia). Results suggest that females may use egg laying as a mechanism to excrete mercury, with eggs having higher concentrations than the corresponding somatic tissue. Organic mercury makes up a minor percentage of total mercury (15-37%) with the percentage being greater in adults than in juveniles. When compared to euphausiids from other parts of the world, the concentration of mercury in Antarctic krill is within the same range, or higher, highlighting the global distribution of this contaminant. Given the high potential for biomagnification of mercury through food webs, concentrations in Antarctic krill may have deleterious effects on long-lived Antarctic krill predators., (Copyright © 2019. Published by Elsevier Ltd.)

Self-sustaining autocatalytic networks play a central role in living systems, from metabolism at the origin of life, simple RNA networks and the modern cell, to ecology and cognition. A collectively autocatalytic network that can be sustained from an ambient food set is also referred to more formally as a 'reflexively autocatalytic food-generated' (RAF) set. In this paper, we first investigate a simplified setting for studying RAFs, which is nevertheless relevant to real biochemistry and which allows an exact mathematical analysis based on graph-theoretic concepts. This, in turn, allows for the development of efficient (polynomial-time) algorithms for questions that are computationally intractable (NP-hard) in the general RAF setting. We then show how this simplified setting for RAF systems leads naturally to a more general notion of RAFs that are 'generative' (they can be built up from simpler RAFs) and for which efficient algorithms carry over to this more general setting. Finally, we show how classical RAF theory can be extended to deal with ensembles of catalysts as well as the assignment of rates to reactions according to which catalysts (or combinations of catalysts) are available.

Essential metabolic reactions are shaping constituents of metabolic networks, enabling viable and distinct phenotypes across diverse life forms. Here we analyse and compare modelling predictions of essential metabolic functions with experimental data and thereby identify core metabolic pathways in prokaryotes. Simulations of 15 manually curated genome-scale metabolic models were integrated with 36 large-scale gene essentiality datasets encompassing a wide variety of species of bacteria and archaea. Conservation of metabolic genes was estimated by analysing 79 representative genomes from all the branches of the prokaryotic tree of life. We find that essentiality patterns reflect phylogenetic relations both for modelling and experimental data, which correlate highly at the pathway level. Genes that are essential for several species tend to be highly conserved as opposed to non-essential genes which may be conserved or not. The tRNA-charging module is highlighted as ancestral and with high centrality in the networks, followed closely by cofactor metabolism, pointing to an early information processing system supplied by organic cofactors. The results, which point to model improvements and also indicate faults in the experimental data, should be relevant to the study of centrality in metabolic networks and ancient metabolism but also to metabolic engineering with prokaryotes., Competing Interests: The authors have declared that no competing interests exist.

Carbon dioxide enters metabolism via six known CO 2 fixation pathways, of which only one is linear, exergonic in the direction of CO 2 -assimilation, and present in both bacterial and archaeal anaerobes - the Wood-Ljungdahl (WL) or reductive acetyl-CoA pathway. Carbon monoxide (CO) plays a central role in the WL pathway as an energy rich intermediate. Here, we scan the major biochemical reaction databases for reactions involving CO and CO 2 . We identified 415 reactions corresponding to enzyme commission (EC) numbers involving CO 2 , which are non-randomly distributed across different biochemical pathways. Their taxonomic distribution, reversibility under physiological conditions, cofactors and prosthetic groups are summarized. In contrast to CO 2 , only 15 reaction classes involving CO were detected. Closer inspection reveals that CO interfaces with metabolism and the carbon cycle at only two enzymes: anaerobic carbon monoxide dehydrogenase (CODH), a Ni- and Fe-containing enzyme that generates CO for CO 2 fixation in the WL pathway, and aerobic CODH, a Mo- and Cu-containing enzyme that oxidizes environmental CO as an electron source. The CO-dependent reaction of the WL pathway involves carbonyl insertion into a methyl carbon-nickel at the Ni-Fe-S A-cluster of acetyl-CoA synthase (ACS). It appears that no alternative mechanisms to the CO-dependent reaction of ACS have evolved in nearly 4 billion years, indicating an ancient and mechanistically essential role for CO at the onset of metabolism., (© 2018 The Authors. The FEBS Journal published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.)

Background: The origin of eukaryotic cells was an important transition in evolution. The factors underlying the origin and evolutionary success of the eukaryote lineage are still discussed. One camp argues that mitochondria were essential for eukaryote origin because of the unique configuration of internalized bioenergetic membranes that they conferred to the common ancestor of all known eukaryotic lineages. A recent paper by Lynch and Marinov concluded that mitochondria were energetically irrelevant to eukaryote origin, a conclusion based on analyses of previously published numbers of various molecules and ribosomes per cell and cell volumes as a presumed proxy for the role of mitochondria in evolution. Their numbers were purportedly extracted from the literature., Results: We have examined the numbers upon which the recent study was based. We report that for a sample of 80 numbers that were purportedly extracted from the literature and that underlie key inferences of the recent study, more than 50% of the values do not exist in the cited papers to which the numbers are attributed. The published result cannot be independently reproduced. Other numbers that the recent study reports differ inexplicably from those in the literature to which they are ascribed. We list the discrepancies between the recently published numbers and the purported literature sources of those numbers in a head to head manner so that the discrepancies are readily evident, although the source of error underlying the discrepancies remains obscure., Conclusion: The data purportedly supporting the view that mitochondria had no impact upon eukaryotic evolution data exhibits notable irregularities. The paper in question evokes the impression that the published numbers are of up to seven significant digit accuracy, when in fact more than half the numbers are nowhere to be found in the literature to which they are attributed. Though the reasons for the discrepancies are unknown, it is important to air these issues, lest the prominent paper in question become a point source of a snowballing error through the literature or become interpreted as a form of evidence that mitochondria were irrelevant to eukaryote evolution., Reviewers: This article was reviewed by Eric Bapteste, Jianzhi Zhang and Martin Lercher.

On page 234 of this Perspective, '50% decrease' has been corrected online to '50% increase' in the sentence "The pH of surface waters south of 60° S decreased by 0.2 between 2017 and 2070, equivalent to a 50% increase in the concentration of hydrogen ions since the pre-industrial period 1 ."

Rock⁻water⁻carbon interactions germane to serpentinization in hydrothermal vents have occurred for over 4 billion years, ever since there was liquid water on Earth. Serpentinization converts iron(II) containing minerals and water to magnetite (Fe₃O₄) plus H₂. The hydrogen can generate native metals such as awaruite (Ni₃Fe), a common serpentinization product. Awaruite catalyzes the synthesis of methane from H₂ and CO₂ under hydrothermal conditions. Native iron and nickel catalyze the synthesis of formate, methanol, acetate, and pyruvate-intermediates of the acetyl-CoA pathway, the most ancient pathway of CO₂ fixation. Carbon monoxide dehydrogenase (CODH) is central to the pathway and employs Ni⁰ in its catalytic mechanism. CODH has been conserved during 4 billion years of evolution as a relic of the natural CO₂-reducing catalyst at the onset of biochemistry. The carbide-containing active site of nitrogenase-the only enzyme on Earth that reduces N₂-is probably also a relic, a biological reconstruction of the naturally occurring inorganic catalyst that generated primordial organic nitrogen. Serpentinization generates Fe₃O₄ and H₂, the catalyst and reductant for industrial CO₂ hydrogenation and for N₂ reduction via the Haber⁻Bosch process. In both industrial processes, an Fe₃O₄ catalyst is matured via H₂-dependent reduction to generate Fe₅C₂ and Fe₂N respectively. Whether serpentinization entails similar catalyst maturation is not known. We suggest that at the onset of life, essential reactions leading to reduced carbon and reduced nitrogen occurred with catalysts that were synthesized during the serpentinization process, connecting the chemistry of life and Earth to industrial chemistry in unexpected ways.

All known life forms trace back to a last universal common ancestor (LUCA) that witnessed the onset of Darwinian evolution. One can ask questions about LUCA in various ways, the most common way being to look for traits that are common to all cells, like ribosomes or the genetic code. With the availability of genomes, we can, however, also ask what genes are ancient by virtue of their phylogeny rather than by virtue of being universal. That approach, undertaken recently, leads to a different view of LUCA than we have had in the past, one that fits well with the harsh geochemical setting of early Earth and resembles the biology of prokaryotes that today inhabit the Earth's crust., Competing Interests: The authors have declared that no competing interests exist.

We present two narratives on the future of Antarctica and the Southern Ocean, from the perspective of an observer looking back from 2070. In the first scenario, greenhouse gas emissions remained unchecked, the climate continued to warm, and the policy response was ineffective; this had large ramifications in Antarctica and the Southern Ocean, with worldwide impacts. In the second scenario, ambitious action was taken to limit greenhouse gas emissions and to establish policies that reduced anthropogenic pressure on the environment, slowing the rate of change in Antarctica. Choices made in the next decade will determine what trajectory is realized.

In prokaryotes, known mechanisms of lateral gene transfer (transformation, transduction, conjugation, and gene transfer agents) generate new combinations of genes among chromosomes during evolution. In eukaryotes, whose host lineage is descended from archaea, lateral gene transfer from organelles to the nucleus occurs at endosymbiotic events. Recent genome analyses studying gene distributions have uncovered evidence for sporadic, discontinuous events of gene transfer from bacteria to archaea during evolution. Other studies have used traditional models designed to investigate gene family size evolution (Count) to support claims that gene transfer to archaea was continuous during evolution, rather than involving occasional periodic mass gene influx events. Here, we show that the methodology used in analyses favoring continuous gene transfers to archaea was misapplied in other studies and does not recover known events of single simultaneous origin for many genes followed by differential loss in real data: plastid genomes. Using the same software and the same settings, we reanalyzed presence/absence pattern data for proteins encoded in plastid genomes and for eukaryotic protein families acquired from plastids. Contrary to expectations under a plastid origin model, we found that the methodology employed inferred that gene acquisitions occurred uniformly across the plant tree. Sometimes as many as nine different acquisitions by plastid DNA were inferred for the same protein family. That is, the methodology that recovered gradual and continuous lateral gene transfer among lineages for archaea obtains the same result for plastids, even though it is known that massive gains followed by gradual differential loss is the true evolutionary process that generated plastid gene distribution data. Our findings caution against the use of models designed to study gene family size evolution for investigating gene transfer processes, especially when transfers involving more than one gene per event are possible.

The biodiversity, ecosystem services and climate variability of the Antarctic continent and the Southern Ocean are major components of the whole Earth system. Antarctic ecosystems are driven more strongly by the physical environment than many other marine and terrestrial ecosystems. As a consequence, to understand ecological functioning, cross-disciplinary studies are especially important in Antarctic research. The conceptual study presented here is based on a workshop initiated by the Research Programme Antarctic Thresholds - Ecosystem Resilience and Adaptation of the Scientific Committee on Antarctic Research, which focussed on challenges in identifying and applying cross-disciplinary approaches in the Antarctic. Novel ideas and first steps in their implementation were clustered into eight themes. These ranged from scale problems, through risk maps, and organism/ecosystem responses to multiple environmental changes and evolutionary processes. Scaling models and data across different spatial and temporal scales were identified as an overarching challenge. Approaches to bridge gaps in Antarctic research programmes included multi-disciplinary monitoring, linking biomolecular findings and simulated physical environments, as well as integrative ecological modelling. The results of advanced cross-disciplinary approaches can contribute significantly to our knowledge of Antarctic and global ecosystem functioning, the consequences of climate change, and to global assessments that ultimately benefit humankind., (Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.)

Collagen is the most abundant protein found in mammals and it exhibits a low immunogenicity, high biocompatibility and biodegradability when compared with others natural polymers. For this reason, it has been explored for the development of biologically instructive biomaterials with applications for tissue substitution and regeneration. Marine origin collagen has been pursued as an alternative to the more common bovine and porcine origins. This study focused on squid (Teuthoidea: Cephalopoda), particularly the Antarctic squid Kondakovia longimana and the Sub-Antarctic squid Illex argentinus as potential collagen sources. In this study, collagen has been isolated from the skins of the squids using acid-based and pepsin-based protocols, with the higher yield being obtained from I. argentinus in the presence of pepsin. The produced collagen has been characterized in terms of physicochemical properties, evidencing an amino acid profile similar to the one of calf collagen, but exhibiting a less preserved structure, with hydrolyzed portions and a lower melting temperature. Pepsin-soluble collagen isolated from I. argentinus was selected for further evaluation of biomedical potential, exploring its incorporation on poly-ε-caprolactone (PCL) 3D printed scaffolds for the development of hybrid scaffolds for tissue engineering, exhibiting hierarchical features., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Knowledge about sexual segregation and gender-specific, or indeed individual specialization, in marine organisms has improved considerably in the past decade. In this context, we tested the "Intersexual Competition Hypothesis" for penguins by investigating the feeding ecology of Gentoo penguins during their austral winter non-breeding season. We considered this during unusual environmental conditions (i.e. the year 2009 had observations of high sea surface and air temperatures) in comparison with the long term average at Bird Island, South Georgia. Through conventional (i.e. stomach contents) and stable isotopic values from red blood cells, plasma and feathers of both male and female Gentoo penguins, we showed that there were significant differences between sexes, with males feeding mainly on fish (54% by mass) followed by crustaceans (38%) whereas females fed mainly on crustaceans (89% by mass) followed by fish (4%). Themisto gaudichaudii was the most important crustacean prey for males (64% by mass; 82% by number; 53% by frequency of occurrence) and females (63% by mass; 77% by number; 89% by frequency of occurrence), contrasting with all previous studies that found Antarctic krill Euphausia superba were generally the main prey. Stable isotopic data showed that, in terms of habitat use (based on δ 13C), there were significant differences in short-term carbon signatures between males and females (based on plasma and red blood cells), suggesting that both sexes explored different habitats, with females exploring more offshore pelagic waters and males feeding more in coastal benthic waters. Based on δ 15N, males fed on significantly higher trophic level than females (based on plasma and red blood cells), in agreement with our diet results., Thus, Gentoo penguins behave in a similar manner to other non-breeding penguins species (e.g. king, macaroni and rockhopper penguins), albeit at a smaller spatial scale (as they do not disperse as these other penguins do), in that they have a wider habitat and trophic niche during the Antarctic Winter (in comparison to Summer). We also detected individual specialization in feeding/trophic levels for each gender, with certain males feeding mainly on fish and certain females mainly on crustaceans, which may be driven the prevailing environmental conditions that lead individuals to search for alternative prey, and cause sexual diet segregation. Our results provide further information to help improve understanding about sexual segregation and individual specialization of marine organisms, while contributing valuable information on the winter diet for Antarctic monitoring programs and for modelling Antarctic marine food webs.

The phase diagram and the critical behavior of the spin-1 and the spin-3/2 two-dimensional Baxter-Wu model in a crystal field are studied by conventional finite-size scaling and conformal invariance theory. The phase diagram of this model, for the spin-1 case, is qualitatively the same as those of the diluted 4-states Potts model and the spin-1 Blume-Capel model. However, for the present case, instead of a tricritical point one has a pentacritical point for a finite value of the crystal field, in disagreement with previous work based on finite-size calculations. On the other hand, for the spin-3/2 case, the phase diagram is much richer and can present, besides a pentacritical point, an additional multicritical end point. Our results also support that the universality class of the critical behavior of the spin-1 and spin-3/2 Baxter-Wu model in a crystal field is the same as the pure Baxter-Wu model, even at the multicritical points.

Background: Comprehensive genomic profiling of clinical samples by next-generation sequencing (NGS) can identify one or more therapy targets for the treatment of metastatic melanoma (MM) with a single diagnostic test., Methods: NGS was performed on hybridization-captured, adaptor ligation-based libraries using DNA extracted from 4 formalin-fixed paraffin-embedded sections cut at 10 microns from 30 MM cases. The exons of 182 cancer-related genes were fully sequenced using the Illumina HiSeq 2000 at an average sequencing depth of 1098X and evaluated for genomic alterations (GAs) including point mutations, insertions, deletions, copy number alterations, and select gene fusions/rearrangements. Clinically relevant GAs (CRGAs) were defined as those identifying commercially available targeted therapeutics or therapies in registered clinical trials., Results: The 30 American Joint Committee on Cancer Stage IV MM included 17 (57%) male and 13 (43%) female patients with a mean age of 59.5 years (range 41-83 years). All MM samples had at least 1 GA, and an average of 2.7 GA/sample (range 1-7) was identified. The mean number of GA did not differ based on age or sex; however, on average, significantly more GAs were identified in amelanotic and poorly differentiated MM. GAs were most commonly identified in BRAF (12 cases, 40%), CDKN2A (6 cases, 20%), NF1 (8 cases, 26.7%), and NRAS (6 cases, 20%). CRGAs were identified in all patients, and represented 77% of the GA (64/83) detected. The median and mean CRGAs per tumor were 2 and 2.1, respectively (range 1-7)., Conclusion: Comprehensive genomic profiling of MM, using a single diagnostic test, uncovers an unexpectedly high number of CRGA that would not be identified by standard of care testing. Moreover, NGS has the potential to influence therapy selection and can direct patients to enter relevant clinical trials evaluating promising targeted therapies.

The composition of a cell in terms of macromolecular building blocks and other organic molecules underlies the metabolic needs and capabilities of a species. Although some core biomass components such as nucleic acids and proteins are evident for most species, the essentiality of the pool of other organic molecules, especially cofactors and prosthetic groups, is yet unclear. Here we integrate biomass compositions from 71 manually curated genome-scale models, 33 large-scale gene essentiality datasets, enzyme-cofactor association data and a vast array of publications, revealing universally essential cofactors for prokaryotic metabolism and also others that are specific for phylogenetic branches or metabolic modes. Our results revise predictions of essential genes in Klebsiella pneumoniae and identify missing biosynthetic pathways in models of Mycobacterium tuberculosis. This work provides fundamental insights into the essentiality of organic cofactors and has implications for minimal cell studies as well as for modeling genotype-phenotype relations in prokaryotic metabolic networks., (Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.)

Cephalopod beaks found in the diet of predators have been a major source of scientific information. In this study, we evaluated the usefulness of DNA and contaminants analysis (total mercury - T-Hg) in cephalopod beaks in order to assess their applicability as tools in marine ecology studies. We concluded that, when applying DNA techniques to cephalopod beaks from Antarctic squid species, when using flesh attached to those beaks, it was possible to obtain DNA and to successfully identify cephalopod species; DNA was not found on the beaks themselves. This study also showed that it is possible to obtain information on T-Hg concentrations in beaks: the T-Hg concentrations found in the beaks were 6 to 46 times lower than in the flesh of the same cephalopod species. More research on the relationships of mercury concentrations in cephalopod beaks (and other tissues), intra- and inter-specifically, are needed in the future., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

Rationale: The main limitation of isotopic tracking for inferring distribution is the lack of detailed reference maps of the isotopic landscape (i.e. isoscapes) in the marine environment. Here, we attempt to map the marine δ(13) C isoscape for the southwestern sector of the Atlantic Ocean, and assess any temporal variation using the wandering albatross as a model species., Methods: Tracking data and blood and diet samples were collected monthly from wandering albatrosses rearing chicks at Bird Island, South Georgia, during the austral winter between May and October 2009. The δ(13) C and δ(15) N values were measured by mass spectrometry in plasma and blood cells, and related to highly accurate data on individual movements and feeding activity obtained using three types of device: GPS, activity (immersion) loggers and stomach temperature probes., Results: The tracked birds foraged in waters to the north or northwest of South Georgia, including the Patagonian shelf-break, as far as 2000 km from the colony. The foraging region encompassed the two main fronts in the Southern Ocean (Polar and Subantarctic fronts). The δ(13) C values varied by only 2.1 ‰ in plasma and 2.5 ‰ in blood cells, and no relationships were found between the δ(13) C values in plasma and the mean latitude or longitude of landings or feeding events of each individual., Conclusions: The failure to distinguish a major biogeographic gradient in δ(13) C values suggest that these values in the south Atlantic Ocean are fairly homogeneous. There was no substantial variation among months in either the δ(13) C or the δ(15) N values of plasma or blood cells of tracked birds. As birds did not show a significant change in diet composition or foraging areas during the study period, these results provide no evidence for major temporal variation in stable isotope ratios in consumer tissues, or in the regional marine isoscape in the austral winter of 2009., (Copyright © 2015 John Wiley & Sons, Ltd.)

Feathers have been widely used to assess mercury contamination in birds as they reflect metal concentrations accumulated between successive moult periods: they are also easy to sample and have minimum impact on the study birds. Moult is considered the major pathway for mercury excretion in seabirds. Penguins are widely believed to undergo a complete, annual moult during which they do not feed. As penguins lose all their feathers, they are expected to have a low individual-variability in feather mercury concentration as all feathers are formed simultaneously from the same somatic reserves. This assumption is central to penguin studies that use feathers to examine the annual or among-individual variation in mercury concentrations in penguins. To test this assumption, we measured the mercury concentrations in 3-5 body feathers of 52 gentoo penguins (Pygoscelis papua) breeding at Bird Island, South Georgia (54°S 38°W). Twenty-five percent of the penguins studied showed substantial within-individual variation in the amount of mercury in their feathers (Coefficient of Variation: 34.7-96.7%). This variation may be caused by differences in moult patterns among individuals within the population leading to different interpretations in the overall population. Further investigation is now needed to fully understand individual variation in penguins' moult.

We consider the energy flow between a classical one-dimensional harmonic oscillator and a set of N two-dimensional chaotic oscillators, which represents the finite environment. Using linear response theory we obtain an analytical effective equation for the system harmonic oscillator, which includes a frequency dependent dissipation, a shift, and memory effects. The damping rate is expressed in terms of the environment mean Lyapunov exponent. A good agreement is shown by comparing theoretical and numerical results, even for environments with mixed (regular and chaotic) motion. Resonance between system and environment frequencies is shown to be more efficient to generate dissipation than larger mean Lyapunov exponents or a larger number of bath chaotic oscillators.

A quantitative assessment of observed and projected environmental changes in the Southern Ocean (SO) with a potential impact on the marine ecosystem shows: (i) large proportions of the SO are and will be affected by one or more climate change processes; areas projected to be affected in the future are larger than areas that are already under environmental stress, (ii) areas affected by changes in sea-ice in the past and likely in the future are much larger than areas affected by ocean warming. The smallest areas (<1% area of the SO) are affected by glacier retreat and warming in the deeper euphotic layer. In the future, decrease in the sea-ice is expected to be widespread. Changes in iceberg impact resulting from further collapse of ice-shelves can potentially affect large parts of shelf and ephemerally in the off-shore regions. However, aragonite undersaturation (acidification) might become one of the biggest problems for the Antarctic marine ecosystem by affecting almost the entire SO. Direct and indirect impacts of various environmental changes to the three major habitats, sea-ice, pelagic and benthos and their biota are complex. The areas affected by environmental stressors range from 33% of the SO for a single stressor, 11% for two and 2% for three, to <1% for four and five overlapping factors. In the future, areas expected to be affected by 2 and 3 overlapping factors are equally large, including potential iceberg changes, and together cover almost 86% of the SO ecosystem., (© 2014 John Wiley & Sons Ltd.)

Age-related variation in demographic rates is now widely documented in wild vertebrate systems, and has significant consequences for population and evolutionary dynamics. However, the mechanisms underpinning such variation, particularly in later life, are less well understood. Foraging efficiency is a key determinant of fitness, with implications for individual life history trade-offs. A variety of faculties known to decline in old age, such as muscular function and visual acuity, are likely to influence foraging performance. We examine age-related variation in the foraging behaviour of a long-lived, wide-ranging oceanic seabird, the wandering albatross Diomedea exulans. Using miniaturised tracking technologies, we compared foraging trip characteristics of birds breeding at Bird Island, South Georgia. Based on movement and immersion data collected during the incubation phase of a single breeding season, and from extensive tracking data collected in previous years from different stages of the breeding cycle, we found limited evidence for age-related variation in commonly reported trip parameters, and failed to detect signs of senescent decline. Our results contrast with the limited number of past studies that have examined foraging behaviour in later life, since these have documented changes in performance consistent with senescence. This highlights the importance of studies across different wild animal populations to gain a broader perspective on the processes driving variation in ageing rates.

Antarctic and Southern Ocean (ASO) marine ecosystems have been changing for at least the last 30 years, including in response to increasing ocean temperatures and changes in the extent and seasonality of sea ice; the magnitude and direction of these changes differ between regions around Antarctica that could see populations of the same species changing differently in different regions. This article reviews current and expected changes in ASO physical habitats in response to climate change. It then reviews how these changes may impact the autecology of marine biota of this polar region: microbes, zooplankton, salps, Antarctic krill, fish, cephalopods, marine mammals, seabirds, and benthos. The general prognosis for ASO marine habitats is for an overall warming and freshening, strengthening of westerly winds, with a potential pole-ward movement of those winds and the frontal systems, and an increase in ocean eddy activity. Many habitat parameters will have regionally specific changes, particularly relating to sea ice characteristics and seasonal dynamics. Lower trophic levels are expected to move south as the ocean conditions in which they are currently found move pole-ward. For Antarctic krill and finfish, the latitudinal breadth of their range will depend on their tolerance of warming oceans and changes to productivity. Ocean acidification is a concern not only for calcifying organisms but also for crustaceans such as Antarctic krill; it is also likely to be the most important change in benthic habitats over the coming century. For marine mammals and birds, the expected changes primarily relate to their flexibility in moving to alternative locations for food and the energetic cost of longer or more complex foraging trips for those that are bound to breeding colonies. Few species are sufficiently well studied to make comprehensive species-specific vulnerability assessments possible. Priorities for future work are discussed., (© 2014 John Wiley & Sons Ltd.)

The concept of the minimal cell has fascinated scientists for a long time, from both fundamental and applied points of view. This broad concept encompasses extreme reductions of genomes, the last universal common ancestor (LUCA), the creation of semiartificial cells, and the design of protocells and chassis cells. Here we review these different areas of research and identify common and complementary aspects of each one. We focus on systems biology, a discipline that is greatly facilitating the classical top-down and bottom-up approaches toward minimal cells. In addition, we also review the so-called middle-out approach and its contributions to the field with mathematical and computational models. Owing to the advances in genomics technologies, much of the work in this area has been centered on minimal genomes, or rather minimal gene sets, required to sustain life. Nevertheless, a fundamental expansion has been taking place in the last few years wherein the minimal gene set is viewed as a backbone of a more complex system. Complementing genomics, progress is being made in understanding the system-wide properties at the levels of the transcriptome, proteome, and metabolome. Network modeling approaches are enabling the integration of these different omics data sets toward an understanding of the complex molecular pathways connecting genotype to phenotype. We review key concepts central to the mapping and modeling of this complexity, which is at the heart of research on minimal cells. Finally, we discuss the distinction between minimizing the number of cellular components and minimizing cellular complexity, toward an improved understanding and utilization of minimal and simpler cells., (Copyright © 2014, American Society for Microbiology. All Rights Reserved.)

"Deep-sea" cephalopods are here defined as cephalopods that spend a significant part of their life cycles outside the euphotic zone. In this chapter, the state of knowledge in several aspects of deep-sea cephalopod research are summarized, including information sources for these animals, diversity and general biogeography and life cycles, including reproduction. Recommendations are made for addressing some of the remaining knowledge deficiencies using a variety of traditional and more recently developed methods. The types of oceanic gear that are suitable for collecting cephalopod specimens and images are reviewed. Many groups of deep-sea cephalopods require taxonomic reviews, ideally based on both morphological and molecular characters. Museum collections play a vital role in these revisions, and novel (molecular) techniques may facilitate new use of old museum specimens. Fundamental life-cycle parameters remain unknown for many species; techniques developed for neritic species that could potentially be applied to deep-sea cephalopods are discussed. Reproductive tactics and strategies in deep-sea cephalopods are very diverse and call for comparative evolutionary and experimental studies, but even in the twenty-first century, mature individuals are still unknown for many species. New insights into diet and trophic position have begun to reveal a more diverse range of feeding strategies than the typically voracious predatory lifestyle known for many cephalopods. Regular standardized deep-sea cephalopod surveys are necessary to provide insight into temporal changes in oceanic cephalopod populations and to forecast, verify and monitor the impacts of global marine changes and human impacts on these populations., (© 2014 Elsevier Ltd All rights reserved.)

Although mercury bio-amplifies through the food chain and accumulates in top predators, mercury concentrations in tissues of the wandering albatross are greater than in any other vertebrate, including closely related species. In order to explore the alternative explanations for this pattern, we measured total mercury concentrations in feathers, plasma and blood cells of wandering albatrosses of known age, sex and breeding status sampled at South Georgia. Mercury concentrations were low in feathers and blood components of chicks, and higher in the feathers of young pre-breeders than in feathers or blood of older pre-breeders and breeding adults. There was no effect of sex on mercury concentrations in the feathers of pre-breeders or breeding adults, whereas levels were significantly higher in blood cells of breeding females than males. The high feather mercury concentrations of young pre-breeders compared with older birds suggest an increase in moult frequency as birds approach maturity., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

Atmospheric pollutant monitoring constitutes a primordial activity in public policies concerning air quality. In São Paulo State, Brazil, the São Paulo State Environment Company (CETESB) maintains an automatic network which continuously monitors CO, SO(2), NO(x), O(3), and particulate matter concentrations in the air. The monitoring process accuracy is a fundamental condition for the actions to be taken by CETESB. As one of the support systems, a preventive maintenance program for the different analyzers used is part of the data quality strategy. Knowledge of the behavior of analyzer failure times could help optimize the program. To achieve this goal, the failure times of an ozone analyzer-considered a repairable system-were modeled by means of the nonhomogeneous Poisson process. The rate of occurrence of failures (ROCOF) was estimated for the intervals 0-70,800 h and 0-88,320 h, in which six and seven failures were observed, respectively. The results showed that the ROCOF estimate is influenced by the choice of the observation period, t(0) = 70,800 h and t(7) = 88,320 h in the cases analyzed. Identification of preventive maintenance actions, mainly when parts replacement occurs in the last interval of observation, is highlighted, justifying the alteration in the behavior of the inter-arrival times. The performance of a follow-up on each analyzer is recommended in order to record the impact of the performed preventive maintenance program on the enhancement of its useful life.

The diets of Antarctic toothfish Dissostichus mawsoni and Patagonian toothfish Dissostichus eleginoides were examined around the South Sandwich Islands in the Southern Ocean, one of few regions with overlapping populations of the two species. Despite large differences in the proportion of stomachs containing prey (76·2% of D. mawsoni compared to 7·2% of D. eleginoides), diet composition was broadly similar (Schoener overlap index of 74·4% based on prey mass) with finfishes (particularly macrourids and muraenolepidids) and cephalopods (mainly Kondakovia longimana) comprising >90% of the prey mass of both species. Predation rates of the main fish prey, as mean counts per stomach sampled, were spatially correlated with their relative abundance around the islands derived from fishery by-catch data, suggesting a general lack of prey selectivity. This study supports the view that bathyal Dissostichus are opportunistic carnivores and finds that D. mawsoni and D. eleginoides occupy a similar trophic niche and are likely to compete for prey in regions where both are distributed. The large increase in rate of prey occurrence and size of prey in D. mawsoni stomachs relative to D. eleginoides suggests, however, species differences in feeding behaviour, which may reflect the increased metabolic demands of a cold-water adapted physiology. [Correction added after online publication 13 June 2011: spelling of species name corrected]., (© 2011 The Authors. Journal of Fish Biology © 2011 The Fisheries Society of the British Isles.)

The Kondo lattice model enlarged by an antiferromagnetic coupling J AF between the localized spins is here investigated using computational techniques. Our results suggest the existence of a d-wave superconducting phase close to half-filling mediated by antiferromagnetic fluctuations. This establishes a closer connection between theory and heavy fermion experiments than currently provided by the standard Kondo lattice model with J AF=0.

We report the presence of spin dimerization in the ground state of the one-dimensional Kondo lattice model at quarter filling. The emergence of this new phase of the Kondo lattice can be traced to the form of the RKKY interaction between the localized moments and provides the first example of dimerization induced indirectly by itinerant electrons. We propose this dimer ordering as the driving mechanism of the spin-Peierls phase observed in the quasi-one-dimensional organic compounds (Per)2M(mnt)(2) (M=Pt, Pd). Moreover, this suggests that a richer phase diagram than the Doniach paradigm may be needed to accommodate the physics of heavy fermion materials.

The extended and standard t-J models are computationally studied on ladders and planes, with emphasis on the small J/t region. At couplings compatible with photoemission results for undoped cuprates, half-doped stripes separating pi-shifted antiferromagnetic (AF) domains are found, as in Tranquada's interpretation of neutron experiments. Our main result is that the elementary stripe "building block" resembles the properties of one hole at small J/t, with robust AF correlations across the hole induced by the local tendency of the charge to separate from the spin. This suggests that the seed of half-doped stripes already exists in the unusual properties of the insulating parent compound.