The structure of biogenic habitat and epibiotic assemblages associated with the global invasive kelp Undaria pinnatifida in comparison to native macroalgae

Kelp forests dominate temperate and polar rocky coastlines and represent critical marine habitats because they support elevated rates of primary and secondary production and high biodiversity. A major threat to the stability of these ecosystems is the proliferation of non-native species, such as the Japanese kelp Undariapinnatifida (‘Wakame’), which has recently colonised natural habitats in the UK. We quantified the abundance and biomass of U. pinnatifida on a natural rocky reef habitat over 10 months to make comparisons with three native canopy-forming brown algae (Laminaria ochroleuca, Saccharina latissima, and Saccorhiza polyschides). We also examined the biogenic habitat structure provided by, and epibiotic assemblages associated with, U. pinnatifida in comparison to native macroalgae. Surveys conducted within the Plymouth Sound Special Area of Conservation indicated that U. pinnatifida is now a dominant and conspicuous member of kelp-dominated communities on natural substrata. Crucially, U. pinnatifida supported a structurally dissimilar and less diverse epibiotic assemblage than the native perennial kelp species. However, U. pinnatifida-associated assemblages were similar to those associated with Saccorhiza polyschides, which has a similar life history and growth strategy. Our results suggest that a shift towards U. pinnatifida dominated reefs could result in impoverished epibiotic assemblages and lower local biodiversity, although this could be offset, to some extent, by the climate-driven proliferation of L. ochroleuca at the poleward range edge, which provides complex biogenic habitat and harbours relatively high biodiversity. Clearly, greater understanding of the long-term dynamics and competitive interactions between these habitat-forming species is needed to accurately predict future biodiversity patterns.

Structure et biogéographie des communautés de pico- et de nanoeurcaryotes pélagiques autour de l'archipel du Svalbard

L’Arctique s’est réchauffé rapidement et il y a urgence d’anticiper les effets que cela pourrait avoir sur les protistes à la base de la chaîne alimentaire. Le phytoplancton de l’Océan Arctique inclut les pico- et nano-eucaryotes (0.45-10 μm diamètre de la cellule) et plusieurs de ceux-ci sont des écotypes retrouvés seulement dans l’Arctique alors que d’autres sont introduits des océans plus méridionaux. Alors que les océans tempérés pénètrent dans l’Arctique, il devient pertinent de savoir si ces communautés microbiennes pourraient être modifiées. L’archipel du Svalbard est une région idéale pour observer la biogéographie des communautés microbiennes sous l’influence de processus polaires et tempérés. Bien qu’ils soient géographiquement proches, les régions côtières entourant le Svalbard sont sujettes à des intrusions alternantes de masses d’eau de l’Arctique et de l’Atlantique en plus des conditions locales. Huit sites ont été échantillonnés en juillet 2013 pour identifier les protistes selon un gradient de profondeur et de masses d’eau autour de l’archipel. En plus des variables océanographiques standards, l’eau a été échantillonnée pour synthétiser des banques d’amplicons ciblant le 18S SSU ARNr et son gène pour ensuite être séquencées à haut débit. Cinq des sites d’étude avaient de faibles concentrations de chlorophylle avec des compositions de communauté post-efflorescence dominée par les dinoflagellés, ciliés, des alvéolés parasites putatifs, chlorophycées et prymnesiophytées. L’intrusion des masses d’eau et les conditions environnementales locales étaient corrélées avec la structure des communautés ; l’origine de la masse d’eau contribuant le plus à la distance phylogénétique des communautés microbiennes. Au sein de trois fjords, de fortes concentrations de chlorophylle sous-entendaient des activités d’efflorescence. Un fjord était dominé par Phaeocystis, un deuxième par un clade arctique identifié comme un Pelagophyceae et un troisième par un assemblage mixte. En général, un signal fort d’écotypes liés à l’Arctique prédominait autour du Svalbard.

Influência dos obstáculos de pequena dimensão na estruturação dos agrupamentos piscícolas: The impact of small physical obstacles on the structure of freshwater fish assemblages

O efeito das grandes barragens na comunidade piscícola vem sendo documentado por numerosos estudos, enquanto o número de trabalhos que incidem sobre o efeito dos obstáculos de pequena dimensão é bastante mais reduzido. A comunidade piscícola foi amostrada e as variáveis ambientais foram caracterizadas em 28 locais divididos por dois cursos de água da Península Ibérica, 14 dos quais localizados imediatamente a montante, jusante e entre cinco pequenos obstáculos na Ribeira de Muge e 14 na Ribeira de Erra, considerada a linha de água de referência. Através de análise estatística multivariada foi possível verificar que variáveis de habitat como a velocidade de corrente e a profundidade, e não as variáveis físico-químicas, foram as principais responsáveis pela discriminação dos vários grupos de locais nas duas ribeiras. A ribeira de referência exibiu um gradiente longitudinal de velocidade de corrente que, contudo, não era suficientemente forte para causar alterações significativas na composição e estrutura dos agrupamentos piscícolas. Através da sucessiva e drástica repetição deste gradiente junto a cada estrutura, a ribeira com obstáculos apresentou diferenças na fauna piscícola entre os três tipos de locais. Os troços lênticos a montante apresentavam uma densidade mais elevada de espécies limnofilicas, omnívoras e exóticas, como o góbio (Gobio lozanoi), que estão bem adaptadas a este tipo de habitat. Os locais de amostragem situados a jusante e entre os obstáculos caracterizavam-se pela dominância de taxa reófilos e invetivo-os (i.e. barbo, Luciobarbus bocagei). As métricas relacionadas com a riqueza específica não apresentaram diferenças entre os três tipos de locais, ao contrário da diversidade que foi mais elevada nos pontos situados entre os obstáculos, afastados da sua influência directa, onde a diversidade de habitats também é mais elevada. Contrariamente aos locais a montante, os troços a jusante e entre os obstáculos apresentaram similaridades, em muitas das características estudadas, com a ribeira de referência, sugerindo que este tipo de estruturas provoca uma alteração mais significativa na comunidade piscícola a montante. Este estudo sugere que os efeitos dos pequenos obstáculos no habitat e na ictiofauna são, em parte, semelhantes aos descritos para as grandes barragens, fornecendo considerações importantes para os esforços de conservação dos ecossistemas ribeirinhos. ABSTRACT; Many studies have assessed the effects of large dams on fishes but few have examined the effects of small obstacles. Fishes were sampled and environmental variables were characterized at 28 sites in two lberian streams, 14 located immediately downstream, upstream and between five small obstacles at River Muge and 14 at River Erra, considered as the reference stream. Multivariate analysis indicated that habitat variables like current velocity and depth, but not physicochemistry, were the main responsible for site groups' discrimination in both streams. The reference stream exhibited a longitudinal gradient of current velocity that, however, wasn't strong enough to cause significant changes in the fish assemblage's composition and structure. By successive and drastically repeating this gradient near each structure, the obstac1es stream presented differences in fish fauna between the three site types. Lentic upstream sites presented higher density of limnophilic, omnivorous and exotic species, like gudgeon Gobio lozanoi, who are well adapted to this type of habitat. Downstream and between obstacles sites were characterized by the dominance of rheophilic and invertivorous taxa, especially barbel Luciobarbus bocagei. Richness metrics did not differ among site types, but diversity was higher in sites located between the obstacles away from its direct influence, where the habitat diversity was higher. Contrarily to upstream sites, downstream and between obstacles sites were similar in many of the studied features to the reference stream, implying that this type of structures cause a higher modification in the upstream fish community. This study suggests that the effects of small obstacles on habitat and fishes are similar, in some extent, to those reported for larger dams, providing important considerations for riverine ecosystem conservation efforts.

Structure and temporal variations of fish assemblages of the Castro Marim salt marsh, southern Portugal

We studied the ichthyofauna of the Castro Marim salt marsh based on monthly sampling surveys at five sites between September 2000 and August 2001. Sampling took place at night during rising neap tides using a 40-m long beach seine. We sampled a total of 7955 fish specimens (37 995.7 g), comprising 34 species and 17 families. The occurrence of most species was occasional, with Pomatoschistus microps (51.9%) and Atherina spp. (10.3%) being the most abundant species, accounting for 62.2% of the total fish captured. Biomass was dominated by the marine species Liza ramado (15.9%), Mullus surmuletus (13.5%), and Liza aurata (13.4%). Temperature and salinity showed a seasonal pattern, with minimums during the winter months and maximums during the summer months. In contrast, river flow peaked in winter and was lowest during summer. This pattern in river flow appears to be correlated with variations in the fish assemblages, which present two distinct compositions during the two periods. A few species characterise the winter fish assemblage, with dominance by residents and the presence of freshwater species, while the summer assemblage is characterised by the presence of many marine visitors that use the salt marsh in their first months/years of life. Temporal variations in total abundance and biomass reflect fluctuations in the dominant species. Resident species presented the highest abundance values, while marine adventitious species and marine species that use the salt marsh as a nursery ground contributed most to community species richness. Castro Marim salt marsh constitutes an important ecosystem for fishes, providing habitat for many species, especially juveniles, which find conditions within the salt marsh suitable for their development. (c) 2006 Elsevier Ltd. All rights reserved.

Composition and temporal dynamics of a temperate rocky cryptobenthic fish assemblage

Temporal variation in a temperate cryptobenthic fish assemblage at the Arrabida Marine Park (Portugal) was assessed by visual Surveys during 2002 and 2003. A total of 9596 fish from 11 families and 30 species was recorded. There were no changes in structure or density at the assemblage level between years, whereas diversity changed significantly due to a higher number of abundant species in the second year. A similar seasonal trend was found between years, with a significant overall density increase in autumn. This is partially explained by the arrival of new recruits of some of the most abundant species in the assemblage. Assemblage diversity and structure also changed across seasons. A group of species encompassing Gobius xanthocephalus, Tripterygion delaisi, Parablennius pilicornis, Gobius paganellus, Lepadogaster candollii and Lepadogaster spp. were analysed in detail. The temporal patterns of two of the most abundant species, G. xanthocephalus and T delaisi, mimicked the overall temporal patterns of the assemblage. We suggest that the inter-annual stability in density of this subtidal fish assemblage may be similar to what has been reported for the intertidal and that strong post-settlement processes are probably shaping this assemblage.

Changes In Chromatin Structure In Nih 3t3 Cells Induced By Valproic Acid And Trichostatin A.

Valproic acid (VPA) and trichostatin A (TSA) are known histone deacetylase inhibitors (HDACIs) with epigenetic activity that affect chromatin supra-organization, nuclear architecture, and cellular proliferation, particularly in tumor cells. In this study, chromatin remodeling with effects extending to heterochromatic areas was investigated by image analysis in non-transformed NIH 3T3 cells treated for different periods with different doses of VPA and TSA under conditions that indicated no loss of cell viability. Image analysis revealed chromatin decondensation that affected not only euchromatin but also heterochromatin, concomitant with a decreased activity of histone deacetylases and a general increase in histone H3 acetylation. Heterochromatin protein 1-α (HP1-α), identified immunocytochemically, was depleted from the pericentromeric heterochromatin following exposure to both HDACIs. Drastic changes affecting cell proliferation and micronucleation but not alteration in CCND2 expression and in ratios of Bcl-2/Bax expression and cell death occurred following a 48-h exposure of the NIH 3T3 cells particularly in response to higher doses of VPA. Our results demonstrated that even low doses of VPA (0.05 mM) and TSA (10 ng/ml) treatments for 1 h can affect chromatin structure, including that of the heterochromatin areas, in non-transformed cells. HP1-α depletion, probably related to histone demethylation at H3K9me3, in addition to the effect of VPA and TSA on histone H3 acetylation, is induced on NIH 3T3 cells. Despite these facts, alterations in cell proliferation and micronucleation, possibly depending on mitotic spindle defects, require a longer exposure to higher doses of VPA and TSA.

Matrix Metalloproteinases And Left Ventricular Function And Structure In Spinal Cord Injured Subjects.

Subjects with spinal cord injury (SCI) exhibit impaired left ventricular (LV) diastolic function, which has been reported to be attenuated by regular physical activity. This study investigated the relationship between circulating matrix metalloproteinases (MMPs) and tissue inhibitors of MMPs (TIMPs) and echocardiographic parameters in SCI subjects and the role of physical activity in this regard. Forty-two men with SCI [19 sedentary (S-SCI) and 23 physically-active (PA-SCI)] were evaluated by clinical, anthropometric, laboratory, and echocardiographic analysis. Plasmatic pro-MMP-2, MMP-2, MMP-8, pro-MMP-9, MMP-9, TIMP-1 and TIMP-2 levels were determined by enzyme-linked immunosorbent assay and zymography. PA-SCI subjects presented lower pro-MMP-2 and pro-MMP-2/TIMP-2 levels and improved markers of LV diastolic function (lower E/Em and higher Em and E/A values) than S-SCI ones. Bivariate analysis showed that pro-MMP-2 correlated inversely with Em and directly with E/Em, while MMP-9 correlated directly with LV mass index and LV end-diastolic diameter in the whole sample. Following multiple regression analysis, pro-MMP-2, but not physical activity, remained associated with Em, while MMP-9 was associated with LV mass index in the whole sample. These findings suggest differing roles for MMPs in LV structure and function regulation and an interaction among pro-MMP-2, diastolic function and physical activity in SCI subjects.

Growth Factor Stimulation Improves The Structure And Properties Of Scaffold-free Engineered Auricular Cartilage Constructs.

The reconstruction of the external ear to correct congenital deformities or repair following trauma remains a significant challenge in reconstructive surgery. Previously, we have developed a novel approach to create scaffold-free, tissue engineering elastic cartilage constructs directly from a small population of donor cells. Although the developed constructs appeared to adopt the structural appearance of native auricular cartilage, the constructs displayed limited expression and poor localization of elastin. In the present study, the effect of growth factor supplementation (insulin, IGF-1, or TGF-β1) was investigated to stimulate elastogenesis as well as to improve overall tissue formation. Using rabbit auricular chondrocytes, bioreactor-cultivated constructs supplemented with either insulin or IGF-1 displayed increased deposition of cartilaginous ECM, improved mechanical properties, and thicknesses comparable to native auricular cartilage after 4 weeks of growth. Similarly, growth factor supplementation resulted in increased expression and improved localization of elastin, primarily restricted within the cartilaginous region of the tissue construct. Additional studies were conducted to determine whether scaffold-free engineered auricular cartilage constructs could be developed in the 3D shape of the external ear. Isolated auricular chondrocytes were grown in rapid-prototyped tissue culture molds with additional insulin or IGF-1 supplementation during bioreactor cultivation. Using this approach, the developed tissue constructs were flexible and had a 3D shape in very good agreement to the culture mold (average error <400 µm). While scaffold-free, engineered auricular cartilage constructs can be created with both the appropriate tissue structure and 3D shape of the external ear, future studies will be aimed assessing potential changes in construct shape and properties after subcutaneous implantation.

Ssr-based Genetic Diversity And Structure Of Garlic Accessions From Brazil.

Garlic is a spice and a medicinal plant; hence, there is an increasing interest in 'developing' new varieties with different culinary properties or with high content of nutraceutical compounds. Phenotypic traits and dominant molecular markers are predominantly used to evaluate the genetic diversity of garlic clones. However, 24 SSR markers (codominant) specific for garlic are available in the literature, fostering germplasm researches. In this study, we genotyped 130 garlic accessions from Brazil and abroad using 17 polymorphic SSR markers to assess the genetic diversity and structure. This is the first attempt to evaluate a large set of accessions maintained by Brazilian institutions. A high level of redundancy was detected in the collection (50 % of the accessions represented eight haplotypes). However, non-redundant accessions presented high genetic diversity. We detected on average five alleles per locus, Shannon index of 1.2, HO of 0.5, and HE of 0.6. A core collection was set with 17 accessions, covering 100 % of the alleles with minimum redundancy. Overall FST and D values indicate a strong genetic structure within accessions. Two major groups identified by both model-based (Bayesian approach) and hierarchical clustering (UPGMA dendrogram) techniques were coherent with the classification of accessions according to maturity time (growth cycle): early-late and midseason accessions. Assessing genetic diversity and structure of garlic collections is the first step towards an efficient management and conservation of accessions in genebanks, as well as to advance future genetic studies and improvement of garlic worldwide.

The Atomic Structure Of A Bare Buffer Layer On Sic(0001) Chemically Resolved.

A chemical-specific photoelectron diffraction structure determination of a carbon rich buffer layer on SiC is reported. In addition to the long-range ripple of this surface, a local buckling in the hexagonal sublattice, which breaks the local range order symmetry, was unraveled.

Crystal Structure Of (3e)-3-[(4-nitro-phen-oxy)-meth-yl]-4-phenyl-but-3-en-2-one.

In the title compound, C17H15NO4, the conformation about the C=C double bond [1.348 (2) Å] is E with the ketone group almost co-planar [C-C-C-C torsion angle = 7.2 (2)°] but the phenyl group twisted away [C-C-C-C = 160.93 (17)°]. The terminal aromatic rings are almost perpendicular to each other [dihedral angle = 81.61 (9)°] giving the mol-ecule an overall U-shape. The crystal packing feature benzene-C-H⋯O(ketone) contacts that lead to supra-molecular helical chains along the b axis. These are connected by π-π inter-actions between benzene and phenyl rings [inter-centroid distance = 3.6648 (14) Å], resulting in the formation of a supra-molecular layer in the bc plane.

Crystal Structure Of (3e)-3-(2,4-di-nitro-phen-oxy-meth-yl)-4-phenyl-but-3-en-2-one.

In the title compound, C17H14N2O6, the conformation about the C=C double bond [1.345 (2) Å] is E, with the ketone moiety almost coplanar [C-C-C-C torsion angle = 9.5 (2)°] along with the phenyl ring [C-C-C-C = 5.9 (2)°]. The aromatic rings are almost perpendicular to each other [dihedral angle = 86.66 (7)°]. The 4-nitro moiety is approximately coplanar with the benzene ring to which it is attached [O-N-C-C = 4.2 (2)°], whereas the one in the ortho position is twisted [O-N-C-C = 138.28 (13)°]. The mol-ecules associate via C-H⋯O inter-actions, involving both O atoms from the 2-nitro group, to form a helical supra-molecular chain along [010]. Nitro-nitro N⋯O inter-actions [2.8461 (19) Å] connect the chains into layers that stack along [001].

On The Consistency Of Monte Carlo Track Structure Dna Damage Simulations.

Monte Carlo track structures (MCTS) simulations have been recognized as useful tools for radiobiological modeling. However, the authors noticed several issues regarding the consistency of reported data. Therefore, in this work, they analyze the impact of various user defined parameters on simulated direct DNA damage yields. In addition, they draw attention to discrepancies in published literature in DNA strand break (SB) yields and selected methodologies. The MCTS code Geant4-DNA was used to compare radial dose profiles in a nanometer-scale region of interest (ROI) for photon sources of varying sizes and energies. Then, electron tracks of 0.28 keV-220 keV were superimposed on a geometric DNA model composed of 2.7 × 10(6) nucleosomes, and SBs were simulated according to four definitions based on energy deposits or energy transfers in DNA strand targets compared to a threshold energy ETH. The SB frequencies and complexities in nucleosomes as a function of incident electron energies were obtained. SBs were classified into higher order clusters such as single and double strand breaks (SSBs and DSBs) based on inter-SB distances and on the number of affected strands. Comparisons of different nonuniform dose distributions lacking charged particle equilibrium may lead to erroneous conclusions regarding the effect of energy on relative biological effectiveness. The energy transfer-based SB definitions give similar SB yields as the one based on energy deposit when ETH ≈ 10.79 eV, but deviate significantly for higher ETH values. Between 30 and 40 nucleosomes/Gy show at least one SB in the ROI. The number of nucleosomes that present a complex damage pattern of more than 2 SBs and the degree of complexity of the damage in these nucleosomes diminish as the incident electron energy increases. DNA damage classification into SSB and DSB is highly dependent on the definitions of these higher order structures and their implementations. The authors' show that, for the four studied models, different yields are expected by up to 54% for SSBs and by up to 32% for DSBs, as a function of the incident electrons energy and of the models being compared. MCTS simulations allow to compare direct DNA damage types and complexities induced by ionizing radiation. However, simulation results depend to a large degree on user-defined parameters, definitions, and algorithms such as: DNA model, dose distribution, SB definition, and the DNA damage clustering algorithm. These interdependencies should be well controlled during the simulations and explicitly reported when comparing results to experiments or calculations.

Human Mitochondrial Hsp70 (mortalin): Shedding Light On Atpase Activity, Interaction With Adenosine Nucleotides, Solution Structure And Domain Organization.

The human mitochondrial Hsp70, also called mortalin, is of considerable importance for mitochondria biogenesis and the correct functioning of the cell machinery. In the mitochondrial matrix, mortalin acts in the importing and folding process of nucleus-encoded proteins. The in vivo deregulation of mortalin expression and/or function has been correlated with age-related diseases and certain cancers due to its interaction with the p53 protein. In spite of its critical biological roles, structural and functional studies on mortalin are limited by its insoluble recombinant production. This study provides the first report of the production of folded and soluble recombinant mortalin when co-expressed with the human Hsp70-escort protein 1, but it is still likely prone to self-association. The monomeric fraction of mortalin presented a slightly elongated shape and basal ATPase activity that is higher than that of its cytoplasmic counterpart Hsp70-1A, suggesting that it was obtained in the functional state. Through small angle X-ray scattering, we assessed the low-resolution structural model of monomeric mortalin that is characterized by an elongated shape. This model adequately accommodated high resolution structures of Hsp70 domains indicating its quality. We also observed that mortalin interacts with adenosine nucleotides with high affinity. Thermally induced unfolding experiments indicated that mortalin is formed by at least two domains and that the transition is sensitive to the presence of adenosine nucleotides and that this process is dependent on the presence of Mg2+ ions. Interestingly, the thermal-induced unfolding assays of mortalin suggested the presence of an aggregation/association event, which was not observed for human Hsp70-1A, and this finding may explain its natural tendency for in vivo aggregation. Our study may contribute to the structural understanding of mortalin as well as to contribute for its recombinant production for antitumor compound screenings.

Nectar Robbery By A Hermit Hummingbird: Association To Floral Phenotype And Its Influence On Flowers And Network Structure.

Interactions between flowers and their visitors span the spectrum from mutualism to antagonism. The literature is rich in studies focusing on mutualism, but nectar robbery has mostly been investigated using phytocentric approaches focused on only a few plant species. To fill this gap, we studied the interactions between a nectar-robbing hermit hummingbird, Phaethornis ruber, and the array of flowers it visits. First, based on a literature review of the interactions involving  P. ruber, we characterized the association of floral larceny to floral phenotype. We then experimentally examined the effects of nectar robbing on nectar standing crop and number of visits of the pollinators to the flowers of Canna paniculata. Finally, we asked whether the incorporation of illegitimate interactions into the analysis affects plant-hummingbird network structure. We identified 97 plant species visited by P. ruber and found that P. ruber engaged in floral larceny in almost 30 % of these species. Nectar robbery was especially common in flowers with longer corolla. In terms of the effect on C. paniculata, the depletion of nectar due to robbery by P. ruber was associated with decreased visitation rates of legitimate pollinators. At the community level, the inclusion of the illegitimate visits of P. ruber resulted in modifications of how modules within the network were organized, notably giving rise to a new module consisting of P. ruber and mostly robbed flowers. However, although illegitimate visits constituted approximately 9 % of all interactions in the network, changes in nestedness, modularity, and network-level specialization were minor. Our results indicate that although a flower robber may have a strong effect on the pollination of a particular plant species, the inclusion of its illegitimate interactions has limited capacity to change overall network structure.