School of Science
Department of Biology
PAPERS PUBLISHED IN INTERNATIONAL SCIENTIFIC JOURNALS DURING 2016
| Alguel Y, Amillis S, Leung J, Lambrinidis G, Capaldi S, Scull NJ, Craven G, Iwata S, Armstrong A, Mikros E, et al. (2016) Structure of eukaryotic purine/H(+) symporter UapA suggests a role for homodimerization in transport activity. Nat Commun. 2016 Apr 18;7:11336. doi: 10.1038/ncomms11336 |
| Abstract: The uric acid/xanthine Hþ symporter, UapA, is a high-affinity purine transporter from the filamentous fungus Aspergillus nidulans. Here we present the crystal structure of a genetically stabilized version of UapA (UapA-G411VD1–11) in complex with xanthine. UapA is formed from two domains, a core domain and a gate domain, similar to the previously solved uracil transporter UraA, which belongs to the same family. The structure shows UapA in an inward-facing conformation with xanthine bound to residues in the core domain. Unlike UraA, which was observed to be a monomer, UapA forms a dimer in the crystals with dimer interactions formed exclusively through the gate domain. Analysis of dominant negative mutants is consistent with dimerization playing a key role in transport. We postulate that UapA uses an elevator transport mechanism likely to be shared with other structurally homologous transporters including anion exchangers and prestin. |
| Alguel Y, Cameron AD, Diallinas G, Byrne B. (2016) Transporter oligomerization: form and function. Biochem Soc Trans. 2016 Dec 15;44(6):1737-1744. |
| Abstract: Transporters are integral membrane proteins with central roles in the efficient movement of molecules across biological membranes. Many transporters exist as oligomers in the membrane. Depending on the individual transport protein, oligomerization can have roles in membrane trafficking, function, regulation and turnover. For example, our recent studies on UapA, a nucleobase ascorbate transporter, from Aspergillus nidulans, have revealed both that dimerization of this protein is essential for correct trafficking to the membrane and the structural basis of how one UapA protomer can affect the function of the closely associated adjacent protomer. Here, we review the roles of oligomerization in many particularly well-studied transporters and transporter families. |
| Bravakos P., Kotoulas G., Skaraki K., Pantazidou A, & A. Economou-Amilli (2016) A polyphasic taxonomic approach in isolated strains of Cyanobacteria from thermal springs of Greece. Molecular Phylogenetics& Evolution 98: 147-160. |
| Abstract: Strains of Cyanobacteria isolated from mats of 9 thermal springs of Greece have been studied for their taxonomic evaluation. A polyphasic taxonomic approach was employed which included: morphological observations by light microscopy and scanning electron microscopy, maximum parsimony, maximum likelihood and Bayesian analysis of 16S rDNA sequences, secondary structural comparisons of 16S-23S rRNA Internal Transcribed Spacer sequences, and finally environmental data. The 17 cyanobacterial isolates formed a diverse group that contained filamentous, coccoid and heterocytous strains. These included representatives of the polyphyletic genera of Synechococcus and Phormidium, and the orders Oscillatoriales, Spirulinales, Chroococcales and Nostocales. After analysis, at least 6 new taxa at the genus level provide new evidence in the taxonomy of Cyanobacteria and highlight the abundant diversity of thermal spring environments with many potential endemic species or ecotypes. |
| Chantzistrountsiou X., Tzovenis I.,Parmakelis A. & Economou-Amilli A. (2016) Characterization of Tetraselmis verrucosa f. rubens (Chlorodendrophyceae) strains from coastal lagoons of Western Greece using a multivariate approach.- Phytotaxa 278(3): 225-240 http://dx.doi.org/10.11646/phytotaxa.00.0.0 |
| Abstract: Strains of Tetraselmis, a genus with systematic and biotechnological interest and one of the most prominent genera in marine phytoplankton, were studied. Five strains of T. verrucosa f. rubens, a taxon first documented in coastal lagoons of Greece, are examined herein under a multivariate approach i.e. in relation to their morphological variability under light and transmission electron microscopy (LM and TEM, respectively), and taking into account certain molecular and biochemical attributes as taxonomic markers, including the plastid-encoded rbcL and nuclear-encoded 18S rRNA gene sequences, and the fatty acid profile. The molecular markers were used to verify the phylogenetic position of the strains within the genus Tetraselmis and the class Chlorodendrophyceae. For that purpose, the original Tetraselmis verrucosa f. rubensisolate (CCAP strain 66/6) was included in the analysis. The molecular data are in agreement with the classification based on morphology. The five strains grouped firmly together and formed a monophyletic group with the original T. verrucosa f. rubens isolate. Lipid analysis of the strains was performed using the FAME (Fatty Acid Methyl-Ester) method and the resulting profile might be used as an additional taxonomic marker. |
| Diallinas G. (2016) Dissection of Transporter Function: From Genetics to Structure. Trends Genet. 2016 Sep;32(9):576-90. doi: 10.1016/j.tig.2016.06.003. Epub 2016 Jul 15. |
| Abstract: Transporters are transmembrane proteins mediating the selective uptake or efflux of solutes, metabolites, drugs, or ions across cellular membranes. Despite their immense biological importance in cell nutrition, communication, signaling, and homeostasis, their study remains technically difficult mostly due to their lipid-embedded nature. The study of eukaryotic transporters presents additional complexity due to multiple subcellular control mechanisms that operate to ensure proper membrane traffic, membrane localization, and turnover. Model fungi present unique genetic tools to study eukaryotic transporter function. This review highlights how fungal transporter genetics combined with new methodologies for assaying their cellular expression and function as well as recent structural approaches have led to the functional dissection of selected transporter paradigms in Aspergillus nidulans. |
| Evangelinos M, Martzoukou O, Chorozian K, Amillis S, Diallinas G. (2016) BsdA(Bsd2) -dependent vacuolar turnover of a misfolded version of the UapA transporter along the secretory pathway: Prominent role of selective autophagy. Mol Microbiol. 2016 Feb 24. doi: 10.1111/mmi.13358. |
| Abstract: Transmembrane proteins translocate co-translationally in the endoplasmic reticulum (ER) membrane and traffic as vesicular cargoes, via the Golgi, in their final membrane destination. Misfolding in the ER leads to protein degradation basically through the ERAD/proteasome system. Here, we use a mutant version of the purine transporter UapA (ΔR481) to show that specific misfolded versions of plasma membrane cargoes undergo vacuolar turnover prior to localization in the plasma membrane. We show that non-endocytic vacuolar turnover of ΔR481 is dependent on BsdABsd2 , an ER transmembrane adaptor of HulARsp5 ubiquitin ligase. We obtain in vivo evidence that BsdABsd2 interacts with HulARsp5 and ΔR481, primarily in the ER. Importantly, accumulation of ΔR481 in the ER triggers delivery of the selective autophagy marker Atg8 in vacuoles along with ΔR481. Genetic block of autophagy (atg9Δ, rabOts ) reduces, but does not abolish, sorting of ΔR481 in the vacuoles, suggesting that a fraction of the misfolded transporter might be redirected for vacuolar degradation via the Golgi. Our results support that multiple routes along the secretory pathway operate for the detoxification of Aspergillus nidulans cells from misfolded membrane proteins, and that BsdA is key factor for marking specific misfolded cargoes. |
| Hamati S., Ouaiss A-K, Babikian J., Jawhari M., Tzovenis I., Mouneimne Y., Economou-Amilli A., Abou-Jawdah Y. (2016) Effect of nitrogen and phosphorus amendment on the yield of a Chlorella sp. strain isolated off the Lebanese coast. International Journal of Environmental & Agriculture Research (IJOEAR) ISSN:2454-1850 Vol-2, Issue-8, August- 2016, p. 106-116 |
| Abstract: A strain of microalgae was isolated from phytoplankton samples collected from the sea coast of Amsheet, North Lebanon. Molecular diagnosis based on ribosomal RNA genes showed it to be most closely related to Chlorella sp. (GenBank accession KC188335.1) with over 90 % nucleotide identity. It was then evaluated whether N and P amendments of seawater fertilized with Guillard’s f/2 medium would improve algal growth and production. Addition of nitrogen (30 ppm) and/or phosphorus (2 ppm) to microalgae grown under laboratory conditions in 3L bioreactors resulted in improved biomass yield (mg dry matter/ L) by approximately 48%, and increased protein yield by approximately 56%, from 19.5% to 30.6% of DM content. Total protein yield/L of culture medium was therefore increased by approximately 83%. Total lipid content and carotenoid levels of the microalgal culture were not affected by the N+P amendement, whereas chlorophyll content was almost doubled. When lower levels of N+P supplementations, 10 and 20 ppm N, were tried, the biomass yield was also improved. The experiment was repeated in 20 L bioreactors in a plastic greenhouse, under normal environmental conditions, with an average temperature of 28°C and a maximum temperature of 36°C. At these relatively high temperatures, the growth rate was slowed down, but N supplementations at 10 and 20 ppm resulted in improved dry matter yield by 25 and 45% respectively, and protein content by 17 and 35%, respectively. Knowledge of the optimal culturing conditions of this local Chlorella strain is essential for its efficient production and is expected to serve future environmental and biotechnological purposes. |
| Kalaroni, S., Tsiaras, K., Petihakis, G., Hoteit, I., Economou-Amilli, A., G.Triantafyllou (2016). Data assimilation of depth-distributed satellite chlorophyll-α in two Mediterranean contrasting sites. Journal of Marine Systems 160: 40-53 |
| Abstract: A new approach for processing the remote sensing chlorophyll-α (Chl-α) before assimilating into an ecosystem model is applied in two contrasting, regarding productivity and nutrients availability, Mediterranean sites: the DYFAMED and POSEIDON E1-M3A fixed point open ocean observatories. The new approach derives optically weighted depth-distributed Chl-α profiles from satellite data based on the model simulated Chl-α vertical distribution and light attenuation coefficient. We use the 1D version of the operational ecological 3D POSEIDON model, based on the European Regional Seas Ecosystem Model (ERSEM). The required hydrodynamic properties are obtained (off-line) from the POSEIDON operational 3D hydrodynamic Mediterranean basin scale model. The data assimilation scheme is the Singular Evolutive Interpolated Kalman (SEIK) filter, the ensemble variant of the Singular Evolutive Extended Kalman (SEEK) filter. The performance of the proposed assimilation approach was evaluated against the Chl-α satellite data and the seasonal averages of available in-situ data for nitrate, phosphate and Chl-α. An improvement of the model simulated near-surface and subsurface maximum Chl-α concentrations is obtained, especially at the DYFAMED site. Model nitrate is improved with assimilation, particularly with the new approach assimilating depth-distributed Chl-α, while model phosphate is slightly worse after assimilation. Additional sensitivity experiments were performed, showing a better performance of the new approach under different scenarios of model Chl-α deviation from pseudo-observations of surface Chl-α. |
| Vasiliki Kioupi and Margarita Arianoutsou (2016) Greek Students Research the Effects of Fire on the Soil System through Project-based Learning. Journal of Biological Education dx.doi.org/10.1080/00219266.2015.1117509 |
| Abstract: This study is focused on the development, implementation and evaluation of an environmental education programme for secondary education students. The programme was entitled ‘Τhe effects of fire on the soil system’ and it was implemented during the school period of 2008. Twenty-four (24) students (aged from 15 to 20) coming from Lidoriki Secondary School (Central Greece) participated in the programme, which was based on Project Method. The programme consisted of one theoretical part (achievement of cognitive and affective goals) and one experimental part (achievement of cognitive and psychomotor goals). Initial, formative and summative assessments were implemented during the course of the programme, by means of questionnaires, observation of students’ teamwork and examination of their work sheets. The questionnaire analysis highlighted students’ misconceptions regarding the subject, revealed positive changes in students’ attitudes as a result of their participation in the programme, as well as satisfactory results concerning the acquired knowledge and skills. The experimental results were of significant scientific and educational value. |
| Lamprinou, V., Christodoulou M., Hernandez-Marine M., Parmakelis A. & A. Economou-Amilli (2016) Spelaeonaias gen. nov., a new true-branched cyanobacterium from Cave Vlychada (Diros, Peloponnese, Greece). – Phytotaxa 282(3): 171-185. |
| Abstract: Based on aspects of the classical LM morphology, and a combination of ultrastructural and molecular data, a new true-branched cyanobacterium, i.e. Spelaeonaias floccida Lamprinou, Christodoulou, Hernández-Mariné et Economou-Amilli, gen. nov. sp. nov., is described from the Greek cave Vlychada (part of the ‘Diros’ cave complex, Peloponnese, Greece). The new monospecific genus bears a Y-like type of branching, intercalary heterocytes and terminal heterocytes at the ensheathed hormogonia, thus morphologically resembling Symphyonemopsis. The subaerophytic growth of the ensheathed hormogonia is considered as the autapomorphic feature for Spelaeonaias. The 16S rRNA sequencing revealed that S. floccida forms a well congruent monophyletic cluster along with two stigonematalean strains SA1301 and SP302 from Maltese catacombs (GenBank: HQ917695 and HQ917696 respectively). |
| Lougiakis N, Gavriil ES, Kairis M, Sioupouli G, Lambrinidis G, Benaki D, Krypotou E, Mikros E, Marakos P, Pouli N, Diallinas G. (2016) Design and synthesis of purine analogues as highly specific ligands for FcyB, a ubiquitous fungal nucleobase transporter. Bioorg Med Chem. 2016 Nov 15;24(22):5941-5952. doi: 10.1016/j.bmc.2016.09.055. Epub 2016 Sep 22. |
| Abstract: In the course of our study on fungal purine transporters, a number of new 3-deazapurine analogues have been rationally designed, based on the interaction of purine substrates with the Aspergillus nidulans FcyB carrier, and synthesized following an effective synthetic procedure. Certain derivatives have been found to specifically inhibit FcyB-mediated [(3)H]-adenine uptake. Molecular simulations have been performed, suggesting that all active compounds interact with FcyB through the formation of hydrogen bonds with Asn163, while the insertion of hydrophobic fragments at position 9 and N6 of 3-deazaadenine enhanced the inhibition. |
| Louvrou I. & A. Economou-Amilli (2016) Taxonomic revision of two rare infraspecific taxa of Tryblionella (Nitzschia) marginulata var. didyma (Bacillariophyceae). Nova Hedwigia, 102 (1-2): 1-8. |
| Abstract: The following two diatom taxa found in hydrothermal sites of Milos Island (Greece) – both of them representing new records for the Greek diatom flora – have been revised: (i) Nitzschia marginulata f. elongata is transferred herein as Tryblionella marginulata f. elongata comb. nov., its diagnosis is emended, its nomenclatural history is outlined and its biogeography is provided, and (ii) Nitzschia marginulata f. parva is transferred herein as Tryblionella marginulata f. parva comb. nov., its diagnosis is emended, taxonomic comments are given and its biogeography is provided. |
| Sophia Rhizopoulou (2016) On the botanical content of Hypnerotomachia Poliphili. Botany Letters, 1-11, doi: http://dx.doi.org/10.1080/23818107.2016.1166070 |
| Abstract: This study focuses on botanical features gleaned from the literary source Hypnerotomachia Poliphili (1499); the analysis reveals that Hypnerotomachia Poliphili includes 285 botanical entities associated with 672 textual passages, which have not hitherto been reported. Roses, myrtle, pines, cypresses, laurel, acanthus, oaks, junipers, ivy, thyme, violets, sandalwoods and orange trees are the most frequently cited plants. Shrubs dominate with 43%, while herbs and trees follow with 28% and 26%, respectively. Arbutus, dittany, labdanum, laurel, myrtle, oaks, oleander, wild and cultivated olive trees, oregano, pine, thyme, grapevines are associated with the diversity of Mediterranean ecosystems. In addition, numerous textual passages of Hypnerotomachia Poliphili mentioning flowering and fruiting plants reveal the seasonality of the Mediterranean region. Exotic plants, such as frankincense tree, myrrh, banana, pepper, sandalwood and jasmines are also included. Thorny plants, sharp thistles and cedars are cited in the text as occurring among ancient monuments and historical ruins. The botanical content of Hypnerotomachia Poliphili constitutes an alternate source of botanical observation, which includes historical, allegoric and symbolic information. |
| M. Salis, B. Arca, F. Alcasena, M. Arianoutsou, V. Bacciu, P. Duce, B. Duguy, N. Koutsias, G. Mallinis, I. Mitsopoulos, J.M. Moreno, J. R. Perez, I.R. Urbieta, F. Xystrakis, G. Zavala & D. Spano. (2016) Predicting wildfire spread and behaviour in Mediterranean landscapes. International Journal of Wildland Fire. 25(10):1015-1032. DOI: 10.1071/WF15081 |
| Abstract: The use of spatially explicit fire spread models to assess fire propagation and behaviour has several applications for fire management and research. We used the FARSITE simulator to predict the spread of a set of wildfires that occurred along an east–west gradient of the Euro-Mediterranean countries. The main purpose of this work was to evaluate the overall accuracy of the simulator and to quantify the effects of standard vs custom fuel models on fire simulation performance. We also analysed the effects of different fuel models and slope classes on the accuracy of FARSITE predictions. To run the simulations, several input layers describing each study area were acquired, and their effect on simulation outputs was analysed. Site-specific fuel models and canopy inputs were derived either from existing vegetation information and field sampling or through remote-sensing data. The custom fuel models produced an increase in simulation accuracy, and results were nearly unequivocal for all the case studies examined. We suggest that spatially explicit fire spread simulators and custom fuel models specifically developed for the heterogeneous landscapes of Mediterranean ecosystems can help improve fire hazard mapping and optimise fuel management practices across the Euro-Mediterranean region. |
| Tsiamis K., Gervasini E., D’Amico F., Deriu I., Katsanevakis S., Crocetta F., Zenetos A., Arianoutsou M., Backeljau Th., Bariche M., Bazos I., Bertaccini A., Brundu G., Carrete M. , Ertan Çinar M., Curto G., Faasse M., Jean-Lou Justine J.-L., Király G., Langer M.R., Levitt Y., Panov V.E., Piraino S., Rabitsch R., Roques A., Scalera R., Shenkar N., Sîrbu I., Tricarico E., Vannini A., Vøllestad L.A. , Zikos A. & Cardoso A.-C. (2016) The EASIN Editorial Board: quality assurance, exchange and sharing of alien species information in Europe. Management of Biological Invasions 7, http://dx.doi.org/10.3391/mbi.2016.7.4.02 |
| Abstract: The European Alien Species Information Network (EASIN) aims to facilitate the exploration of alien species information in Europe, and is recognized as the information system supporting European Union Member States in the implementation of the recently published Invasive Alien Species Regulation. In this paper, we present the role and activities of the EASIN Editorial Board (EB), which is responsible for the quality assurance, safeguarding and constant improvement of EASIN. The EB is supported by a web platform that facilitates online discussions about alien species. This platform creates a virtual community by providing a forum-like interface that is moderated by the EB Members but is freely accessible to the scientific community and the general public. It allows all registered users to make comments, raise questions and share experience and expertise on alien species in Europe. Moreover, it provides a means for exchanging opinions and solving disputes in a transparent way. The overall EB activity is commonly agreed upon procedures and standards. |
| C. Ververisa, N.S. Christodoulakis, R. Santas, Ph. Santas, K. Georghiou (2016) Effects of municipal sludge and treated waste water on biomass yieldand fiber properties of kenaf (Hibiscus cannabinus L.). Industrial Crops and Products 84 7–12 dx.doi.org/10.1016/j.indcrop.2016.01.040 |
| Abstract: Kenaf (Hibiscus cannabinus L.) was experimentally cultivated with the use of digested, dried sewage sludge(130 t/ha) and water from a municipal Sewage Treatment Plant (STP) in order to assess their potential toreplace conventional fertilization (100 kg N/ha, 75 kg P2O5/ha and 75 kg K2O/ha) and irrigation. Tap waterand treated wastewater were used for irrigation in quantities corresponding to 6500 m3/ha. Four differenttreatment combinations were applied as follows: (a) wastewater irrigation and conventional fertilization,(b) wastewater irrigation and sewage sludge fertilization, (c) tap water irrigation and sewage sludgefertilization, and (d) tap water irrigation and conventional fertilization. The dry plant biomass collectedin the final harvest (140 days after plant emergence) from the four treatment plots was 12.3 t/ha, 12.6 t/ha,12.4 t/ha and 12.8 t/ha respectively. These differences were not statistically significant (ANOVA, P = 0.05)and, therefore, it was concluded that the use of municipal wastes had similar effects on dry biomassproduction with that of conventional fertilization. An earlier harvest (125 days after plant emergence)gave 11.3% lower dry biomass on average in relation to the second harvest, and this difference wasstatistically significant (ANOVA, P = 0.05). Premature harvest may lead to significant biomass losses, so theplant must be collected during its technological maturity stage. There was not any statistically significantdifference among the four treatments and between the two harvests in fiber dimensions and derivedvalues (suitability indices for paper manufacture). On the other hand, cellulose and lignin content in thesecond harvest were significantly higher compared to the first one, whereas no significant differenceswere detected among the four treatments. |