Polyploid lineages in the genus Porphyra

Whole genome duplication is now accepted as an important evolutionary force, but the genetic factors and the life history implications affecting the existence and abundance of polyploid lineages within species are still poorly known. Polyploidy has been mainly studied in plant model species in which the sporophyte is the dominant phase in their life history. In this study, we address such questions in a novel system (Porphyra, red algae) where the gametophyte is the dominant phase in the life history. Three Porphyra species (P. dioica, P. umbilicalis, and P. linearis) were used in comparisons of ploidy levels, genome sizes and genetic differentiation using flow cytometry and 11 microsatellite markers among putative polyploid lineages. Multiple ploidy levels and genome sizes were found in Porphyra species, representing different cell lines and comprising several cytotype combinations among the same and different individuals. In P. linearis, genetic differentiation was found among three polyploid lineages: triploid, tetraploid and mixoploids, representing different evolutionary units. We conclude that the gametophytic phase (n) in Porphyra species is not haploid, contradicting previous theories. New hypotheses for the life histories of Porphyra species are discussed.FCT (Fundacao para a Ciencia e a Tecnologia, Portugal) [SFRH/BPD/109452/2015, NORIGENOMICS - PTDC/MAR/099698/2008, UID/Multi/04326/2013, BIODIVERSA/004/2015-MARFOR

Some don't like it hot: microhabitat-dependent thermal and water stresses in a trailing edge population

The distributional limits of species in response to environmental change are usually studied at large temporal and/or geographical scales. However, organismal scale habitat variation can be overlooked when investigating large-scale averages of key factors such as temperature. We examine how microhabitat thermal conditions relate to physiological limits, which may contribute to recent range shifts in an intertidal alga. We defined the onset and maximum temperatures of the heat-shock response (HSR) for a southern edge population of Fucus vesiculosus, which has subsequently become extinct. The physiological threshold for resilience (assayed using chlorophyll fluorescence) coincided with declining HSR, determined from the temperature-dependent induction of seven heat-shock protein transcripts. In intertidal habitats, temperature affects physiology directly by controlling body temperature and indirectly through evaporative water loss. We investigated the relationship between the thermal environment and in situ molecular HSR at microhabitat scales. Over cm to m scales, four distinct microhabitats were defined in algal patches (canopy surface, patch edge, subcanopy, submerged channels), revealing distinct thermal and water stress environments during low-tide emersion. The in situ HSR agreed with estimated tissue temperatures in all but one microhabitat. Remarkably, in the most thermally extreme microhabitat (canopy surface), the HSR was essentially absent in desiccated tissue, providing a potential escape from the cellular metabolic costs of thermal stress. Meteorological records, microenvironmental thermal profiles and HSR data indicate that the maximum HSR is approached or exceeded in hydrated tissue during daytime low tides for much of the year. Furthermore, present-day summer seawater temperatures are sufficient to induce HSR during high-tide immersion, preventing recovery and resulting in continuous HSR during daytime low-tide cycles over the entire summer. HSR in the field matched microhabitat temperatures more closely than local seawater or atmospheric data, suggesting that the impacts of climatic change are best understood at the microhabitat scale, particularly in intertidal areas.FCT - Portuguese Science Foundation [POCTI/MAR/61105/2004, EXCL/AAG-GLO/0661/2012, SFRH/BPD/63/03/2009, SFRH/BD/74436/2010]info:eu-repo/semantics/publishedVersio

Evolutionary and Ecological Trees and Networks

Evolutionary relationships between species are usually represented in phylogenies, i.e. evolutionary trees, which are a type of networks. The terminal nodes of these trees represent species, which are made of individuals and populations among which gene flow occurs. This flow can also be represented as a network. In this paper we briefly show some properties of these complex networks of evolutionary and ecological relationships. First, we characterize large scale evolutionary relationships in the Tree of Life by a degree distribution. Second, we represent genetic relationships between individuals of a Mediterranean marine plant, Posidonia oceanica, in terms of a Minimum Spanning Tree. Finally, relationships among plant shoots inside populations are represented as networks of genetic similarity.Comment: 6 pages, 5 figures. To appear in Proceedings of the Medyfinol06 Conferenc

Less is more: seagrass restoration success using less vegetation per area

Seagrass restoration in open coast environments presents unique challenges. Traditional sod transplant designs, though relatively successful in these environments, are impractical for large-scale restoration due to high biomass requirements. Here, we develop the checkers design, which aims to optimise the usage of biomass by transplanting fewer sods in a checkerboard pattern. We established six plots (9 m2 each) for each species (Zostera marina and Zostera noltei), with 25 sods in each plot. The area, percent cover, density, and leaf length were measured at 1, 6, and 12 months. The plots located on the seaward end of the transplant design vanished over the winter, suggesting location-dependent survival influenced by winter storms. Nevertheless, both species exhibited increased percentages of cover, density, and vegetated area after one year, with variations between species. Z. noltei showed a slower expansion but greater resilience to winter, while Z. marina displayed a higher density and cover over the first 6 months but experienced area loss during the winter. Despite these differences, both species survived and increased vegetated areas after one year, indicating the viability and promise of the checkers method for large-scale restoration. However, careful consideration of location or storm-mitigating measures is essential for the successful implementation of this method.LA/P/0101/2020; CRESC Algarve 2020 and COMPETE 2020 through project EMBRC.PT ALG-01-0145-FEDER-022121info:eu-repo/semantics/publishedVersio

Hologenome theory supported by cooccurrence networks of species-specific bacterial communities in siphonous algae (Caulerpa)

The siphonous algae of the Caulerpa genus harbor internal microbial communities hypothesized to play important roles in development, defense and metabolic activities of the host. Here, we characterize the endophytic bacterial community of four Caulerpa taxa in the Mediterranean Sea, through 16S rRNA amplicon sequencing. Results reveal a striking alpha diversity of the bacterial communities, similar to levels found in sponges and coral holobionts. These comprise (1) a very small core community shared across all hosts ( 70%) species-specific fraction of the community, forming very specific clusters revealed by modularity in networks of cooccurrence, even in areas where distinct Caulerpa taxa occurred in sympatry. Indirect inferences based on sequence homology suggest that these communities may play an important role in the metabolism of their host, in particular on their ability to grow on anoxic sediment. These findings support the hologenome theory and the need for a holistic framework in ecological and evolutionary studies of these holobionts that frequently become invasive.Portuguese Foundation for Science and Technology (FCT); FEDER; project IBISA [PTDC / MAR / 64749 / 2006]; PhD fellowship from FCT [SFRH/BD/30043/2006]; FSEinfo:eu-repo/semantics/publishedVersio

kinematic and neurophysiological models future applications in neurorehabilitation

This paper emphasizes the importance of developing kinematic and neurophysiological methods for evaluating motor and functional recovery in the field of neurorehabilitation. From a review of the literature, it is concluded that optoelectronic motion analysis and neurophysiological techniques, such as the study of nociceptive withdrawal reflex, might constitute useful applications for future research

Hybrid Photonic Crystal Fiber Sensing Of High Hydrostatic Pressure

The opto-mechanical response of Hybrid Photonic Crystal Fiber (HPCF) with Ge-doped inclusions is numerically modeled for high hydrostatic pressure sensing purpose. A typical photonic crystal fiber (PCF) consists of a silica solidcore and a cladding with a hexagonal lattice of air-holes. The HPCF is similar to the regular PCF, but a horizontal line of air-holes is substituted by solid high index rods of Ge-doped silica. The optical guidance in HPCFs is supported combining two physical effects: the modified total internal reflection and the photonic bandgap. In such fibers, the Gedoped inclusions induce residual birefringence. In our analysis, we evaluate the susceptibility of the phase modal birefringence and group birefringence to hydrostatic pressure. The analyses were performed at a photonic bandgap with central wavelength near to 1350 nm. The polarimetric pressure sensitivity is about 10 rad/MPa x m at λ = 1175 nm. © 2011 Copyright Society of Photo-Optical Instrumentation Engineers (SPIE).7753Oz Optics,Simbol Test Systems, Inc.,FISO Technologies, Inc.,CMC Microsystems Corporation,Innovative Economy: National Strategic Reference FrameworkCerqueira, A.S., Hybrid photonic crystal fiber (2006) Opt. Express, 14 (2), pp. 926-931Cerqueira, A.S., Recent progress and novel applications of photonic crystal fibers (2010) Rep. Prog. Phys., 73, p. 023301Cerqueira, A.S., Birefringence properties of hybrid photonic crystal fibers (2009) Proceedings of Microwave and Optoelectronics Conference (IMOC 2009), pp. 804-806. , Belem, Brazil, 03-06, NovemberFranco, M.A.R., Thermal tunability of photonic bandgaps in photonic crystal fibers selectively filled with nematic liquid crystal Proceedings of 2nd Workshop on Specialty Optical Fibers and Their Applications (WSOF-2), Oaxaca, Mexico, 13-15, October, (2010)Fleming, J.W., Dispersion in GeO2 -SiO2 glasses (1984) Appl. Opt., 23 (24), pp. 4486-4493Martynkien, T., Highly birefringent microstructured fibers with enhanced sensitivity to hydrostatic pressure (2010) Opt. Express, 18 (14), pp. 15113-15121Kühn, B., Schadrack, R., Thermal expansion of synthetic fused silica as a function of OH content and fictive temperature (2009) J. Non-Cryst. Solids, 355, pp. 323-326Gupta, D., Kumar, A., Thyagarajan, K., Polarization mode dispersion in single mode optical fibers due to core-ellipticity (2006) Opt. Commun., 263, pp. 36-41Koshiba, M., (1992) Optical Waveguide Theory by the Finite Element Method, pp. 133-160. , KTK Scientific Publishers and Kluwer Academic Publishers, TokyoUrbanczyk, W., Martynkien, T., Bock, W.J., Dispersion effects in elliptical-core highly birefringent fibers (2001) Appl. Opt., 40 (12), pp. 1911-1920Olszewski, J., Birefringence analysis in photonic crystal fibers with germanium-doped core (2009) J. Opt. A: Pure Appl. Opt., 11, pp. 1-10Martynkien, T., Urbanczyk, W., Modeling of spectral characteristics of Corning PMF-38 highly birefringent fiber (2002) Optik, 113 (1), pp. 25-30Hlubina, P., Broad spectral range measurements and modelling of birefringence dispersion in two-mode elliptical-core fibres (2010) J. Opt., 12, pp. 1-8Martynkien, T., Birefringence in microstructure fiber with elliptical GeO2 highly doped inclusion in the core (2008) Opt. Lett., 33 (23), pp. 2764-2766Verbandt, Y., Polarimetric Optical Fiber Sensors: Aspects of Sensitivity and Practical Implementation (1997) Opt. Rev., 4 (1 A), pp. 75-79Lagakos, N., Bucaro, J.A., Hughes, R., Acoustic sensitivity predictions of single-mode optical fibers using Brillouin scattering (1980) Appl. Opt., 19 (21), pp. 3668-3670Chiang, K.S., Sceats, Wong, D., Ultraviolet photolytic-induced changes in optical fibers: The thermal expansion coefficient (1993) Opt. Lett., 18 (12), pp. 965-96

Interactions of daylength, temperature and nutrients affect thresholds for life stage transitions in the kelp Laminaria digitata (Phaeophyceae)

Kelp beds worldwide are under pressure from ongoing climate and environmental change. Along European coastlines increases in seawater temperature and changes in nutrient conditions occur where upwelling events are disrupted and also along eutrophicated coasts. In addition, seaweed responses to change may interact with seasonal daylength cycles. We performed a factorial experiment to examine the combined effects of seawater temperatures, nutrient regimes and photoperiod (long and short days) in order to better understand how latitudinal or seasonal differences in daylengths affect the sensitivity of transient microscopic kelp stages of Laminaria digitata from the North Sea to warming and eutrophication. While the optimal temperature range for vegetative gametophyte growth was 10 degrees C-18 degrees C under long summer photoperiod conditions, gametogenesis was induced at lower temperatures between 5 degrees C and 15 degrees C, with maximum sporophyte development under long photoperiods and enriched nutrient regimes, which represent local late spring conditions. Although gametogenesis was fastest at 10 degrees C-15 degrees C, sporophyte recruitment was highest at 5 degrees C. As these particular early life cycle processes in L. digitata have different temperature optima, this may drive the seasonal cycle of recruitment in the field. Increasing summer temperatures due to global warming will increase gametophyte size due to enhanced vegetative growth and inhibition of gametogenesis. This will probably lead to delayed but enhanced recruitment of new sporophytes under cooler autumn to spring conditions over a wide geographical scale, preventing the formation of juvenile sporophytes under stressful summer conditions and possibly changing annual recruitment patterns.STSM Grant from the COST Action "Phycomorph" [FA1406]; Portuguese Science Foundation (FCT) programs [EXCL/AAG-GLO/0661/2012, UID/Multi/04326/2013]; BiodiVERsA [Biodiversa/0004/2015, PTDC/MAR-EST/6053/2014]info:eu-repo/semantics/publishedVersio

Key determinants of target DNA recognition by retroviral intasomes

BACKGROUND: Retroviral integration favors weakly conserved palindrome sequences at the sites of viral DNA joining and generates a short (4–6 bp) duplication of host DNA flanking the provirus. We previously determined two key parameters that underlie the target DNA preference for prototype foamy virus (PFV) and human immunodeficiency virus type 1 (HIV-1) integration: flexible pyrimidine (Y)/purine (R) dinucleotide steps at the centers of the integration sites, and base contacts with specific integrase residues, such as Ala188 in PFV integrase and Ser119 in HIV-1 integrase. Here we examined the dinucleotide preference profiles of a range of retroviruses and correlated these findings with respect to length of target site duplication (TSD). RESULTS: Integration datasets covering six viral genera and the three lengths of TSD were accessed from the literature or generated in this work. All viruses exhibited significant enrichments of flexible YR and/or selection against rigid RY dinucleotide steps at the centers of integration sites, and the magnitude of this enrichment inversely correlated with TSD length. The DNA sequence environments of in vivo-generated HIV-1 and PFV sites were consistent with integration into nucleosomes, however, the local sequence preferences were largely independent of target DNA chromatinization. Integration sites derived from cells infected with the gammaretrovirus reticuloendotheliosis virus strain A (Rev-A), which yields a 5 bp TSD, revealed the targeting of global chromatin features most similar to those of Moloney murine leukemia virus, which yields a 4 bp duplication. In vitro assays revealed that Rev-A integrase interacts with and is catalytically stimulated by cellular bromodomain containing 4 protein. CONCLUSIONS: Retroviral integrases have likely evolved to bend target DNA to fit scissile phosphodiester bonds into two active sites for integration, and viruses that cut target DNA with a 6 bp stagger may not need to bend DNA as sharply as viruses that cleave with 4 bp or 5 bp staggers. For PFV and HIV-1, the selection of signature bases and central flexibility at sites of integration is largely independent of chromatin structure. Furthermore, global Rev-A integration is likely directed to chromatin features by bromodomain and extraterminal domain proteins. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12977-015-0167-3) contains supplementary material, which is available to authorized users