Analysis of genetic variation among accessions of critically endangered Rhaponticoides iconiensis and Rhaponticoides mykalea based on RAPD and SDSPAGE markers

Rhaponticoides iconiensis (Hub.-Mor.) M.V.Agab and Greuter is a rare and endangered endemic species of the Konya region of Turkey. One related taxon, Rhaponticoides mykalea (Hub.-Mor.) M.V.Agab andGreuter, is morphologically similar but occurs in different geographical locations. This study has been conducted on the biology of this threatened plant in order to understand better the factors that shouldbe included in the development of conservation practices. The genetic variations were studied using RAPD markers and SDS-PAGE profiles of total seed proteins for three R. iconiensis populations and two R. mykalea populations. The analyzed R. iconiensis populations belonged to different soil types (calcareous and volcanic). The analyzed R. iconiensis and R. mykalea populations belonged to different bioclimatic zones. A genetic diversity within populations was detected both by SDS-PAGE and RAPD for R. iconiensis populations. The level of variation did not differ with respect to soil type for the species studied. Populations collected from the same soil types carried more polymorphisms than those grown in different zones. The genetic diversity was revealed more clearly for all populations byRAPD than through analyzing proteins. Differentiation between ecological groups was higher than that revealed within groups. Conservation programs should take into account the level of genetic diversity within population revealed by these markers according to soil types

Measures and Limits of Models of Fixation Selection

Models of fixation selection are a central tool in the quest to understand how the human mind selects relevant information. Using this tool in the evaluation of competing claims often requires comparing different models' relative performance in predicting eye movements. However, studies use a wide variety of performance measures with markedly different properties, which makes a comparison difficult. We make three main contributions to this line of research: First we argue for a set of desirable properties, review commonly used measures, and conclude that no single measure unites all desirable properties. However the area under the ROC curve (a classification measure) and the KL-divergence (a distance measure of probability distributions) combine many desirable properties and allow a meaningful comparison of critical model performance. We give an analytical proof of the linearity of the ROC measure with respect to averaging over subjects and demonstrate an appropriate correction of entropy-based measures like KL-divergence for small sample sizes in the context of eye-tracking data. Second, we provide a lower bound and an upper bound of these measures, based on image-independent properties of fixation data and between subject consistency respectively. Based on these bounds it is possible to give a reference frame to judge the predictive power of a model of fixation selection . We provide open-source python code to compute the reference frame. Third, we show that the upper, between subject consistency bound holds only for models that predict averages of subject populations. Departing from this we show that incorporating subject-specific viewing behavior can generate predictions which surpass that upper bound. Taken together, these findings lay out the required information that allow a well-founded judgment of the quality of any model of fixation selection and should therefore be reported when a new model is introduced

Predicting Eye Fixations on Complex Visual Stimuli Using Local Symmetry

Most bottom-up models that predict human eye fixations are based on contrast features. The saliency model of Itti, Koch and Niebur is an example of such contrast-saliency models. Although the model has been successfully compared to human eye fixations, we show that it lacks preciseness in the prediction of fixations on mirror-symmetrical forms. The contrast model gives high response at the borders, whereas human observers consistently look at the symmetrical center of these forms. We propose a saliency model that predicts eye fixations using local mirror symmetry. To test the model, we performed an eye-tracking experiment with participants viewing complex photographic images and compared the data with our symmetry model and the contrast model. The results show that our symmetry model predicts human eye fixations significantly better on a wide variety of images including many that are not selected for their symmetrical content. Moreover, our results show that especially early fixations are on highly symmetrical areas of the images. We conclude that symmetry is a strong predictor of human eye fixations and that it can be used as a predictor of the order of fixation

The Biodiversity of the Mediterranean Sea: Estimates, Patterns, and Threats

The Mediterranean Sea is a marine biodiversity hot spot. Here we combined an extensive literature analysis with expert opinions to update publicly available estimates of major taxa in this marine ecosystem and to revise and update several species lists. We also assessed overall spatial and temporal patterns of species diversity and identified major changes and threats. Our results listed approximately 17,000 marine species occurring in the Mediterranean Sea. However, our estimates of marine diversity are still incomplete as yet—undescribed species will be added in the future. Diversity for microbes is substantially underestimated, and the deep-sea areas and portions of the southern and eastern region are still poorly known. In addition, the invasion of alien species is a crucial factor that will continue to change the biodiversity of the Mediterranean, mainly in its eastern basin that can spread rapidly northwards and westwards due to the warming of the Mediterranean Sea. Spatial patterns showed a general decrease in biodiversity from northwestern to southeastern regions following a gradient of production, with some exceptions and caution due to gaps in our knowledge of the biota along the southern and eastern rims. Biodiversity was also generally higher in coastal areas and continental shelves, and decreases with depth. Temporal trends indicated that overexploitation and habitat loss have been the main human drivers of historical changes in biodiversity. At present, habitat loss and degradation, followed by fishing impacts, pollution, climate change, eutrophication, and the establishment of alien species are the most important threats and affect the greatest number of taxonomic groups. All these impacts are expected to grow in importance in the future, especially climate change and habitat degradation. The spatial identification of hot spots highlighted the ecological importance of most of the western Mediterranean shelves (and in particular, the Strait of Gibraltar and the adjacent Alboran Sea), western African coast, the Adriatic, and the Aegean Sea, which show high concentrations of endangered, threatened, or vulnerable species. The Levantine Basin, severely impacted by the invasion of species, is endangered as well

Taxonomic relationships in genus Fritillaria (Liliaceae): Evidence from RAPD-PCR and SDS-PAGE of seed proteins

The genus Fritillaria L. is one of the examples from the several unsolved taxonomic problems. The classical identification of plant depends on morphological characteristics. Therefore, it is difficult to determine the botanical origin of some plants. The goals of this study were to examine the taxonomic status of these 42 taxa of Fritillaria in Turkey by means of RAPD-PCR and seed protein analysis in addition to taxonomic interpretation of species. SDS-PAGE and RAPD-PCR techniques were used to help taxonomic interpretation of Fritillaria species. Dendrogram based on genetic distances was calculated using the computer programmed PopGen. For the RAPD-PCR analysis, 40 random primers were tested in the amplification reactions with Fritillaria species. Only 9 of them gave consistently reproducible banding patterns. The analysis of seed proteins showed that all studied genotypes had a specific protein pattern except the species that were close to each other based on morphological data. In electrophoretic protein banding patterns a total of 22-30 protein bands were observed. The protein bands in the region between 116-66 kDa were almost similar in all the species tested. In addition to that, all the species of Fritillaria had two bands in common (just bigger than 25 kDa). F. acmopetala subsp. acmopetala and F. sororum are very close relatives according to morphological, RAPD and protein results. Therefore these two taxa can be considered as synonyms. F. zagrica, F. caucasica, F. baskilensis, F. armena and F. pinardii are grouped together. All these separate species treated as synonyms based on morphological and molecular data. © 2008 Akadémiai Kiadó

Taxonomic relationships in genus Fritillaria (Liliaceae): Evidence from RAPD-PCR and SDS-PAGE of seed proteins

The genus Fritillaria L. is one of the examples from the several unsolved taxonomic problems. The classical identification of plant depends on morphological characteristics. Therefore, it is difficult to determine the botanical origin of some plants. The goals of this study were to examine the taxonomic status of these 42 taxa of Fritillaria in Turkey by means of RAPD-PCR and seed protein analysis in addition to taxonomic interpretation of species. SDS-PAGE and RAPD-PCR techniques were used to help taxonomic interpretation of Fritillaria species. Dendrogram based on g enetic distances was calculated using the computer programmed PopGen. For the RAPD-PCR analysis, 40 random primers were tested in the amplification reactions with Fritillaria species. Only 9 of them gave consistently reproducible banding patterns. The analysis of seed proteins showed that all studied genotypes had a specific protein pattern except the species that were close to each other based on morphological data. In electrophoretic protein banding patterns a total of 22–30 protein bands were observed. The protein bands in the region between 116-66 kDa were almost similar in all the species tested. In addition to that, all the species of Fritillaria had two bands in common (just bigger than 25 kDa). F. acmopetala subsp. acmopetala and F. sororum are very close relatives according to morphological, RAPD and protein results. Therefore these two taxa can be considered as synonyms. F. zagrica , F. caucasica , F. baskilensis , F. armena and F. pinardii are grouped together. All these separate species treated as synonyms based on morphological and molecular data

Cephalaria duzceënsis (Dipsacaceae), a new species from the western Black Sea region, Turkey

A new species, Cephalaria duzceënsis N. Aksoy & R. S. Göktürk (Dipsacacae) from western Black Sea region of Turkey is described. It is illustrated in line drawings and the morphology of the new species is compared with Cephalaria speciosa. Molecular and morphological methods were used to separate the two species. Both species were first identified morphologically and then studied by randomly amplified polymorphic DNA (RAPD) markers. Genetic similarities were calculated based on the RAPD data and used to construct a UPGMA dendrogram. According to the result, two main clusters were observed using the character differences. It is concluded that C. duzceënsis sp. nov. is different from C. speciosa. © 2007 The Authors

Antioxidant and antimicrobial activities of Solidago virgaurea extracts

Solidago virgaurea is an herbaceous perennial plant of the family Asteraceae. It has been traditionally used to terat urinary tract, nephrolithiasis and prostate. Our objective was to determine the antioxidant activities, reducing powers, 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical-scaenging activities and antimicrobial activities of metanol and hot water extracts of S. virgaurea from Bursa region in Turkey. The highest antioxidant activity was found in the metanol extract. The reducing power of the metanol extract was the highest, but its reducing power was markedly lower than that of ascorbic acid. Thehighest DPPH radical-scavenging activity was found in the metanol, with 50% DPPH radical scavenging at a concentration of 74.66 ìgml-1 dried metanol extract, while at the same concentration of dried waterextract the value was 22.16%. Metanol extract of S. virgaurea showed antimicrobial activities against Staphylococcus aureus, Enterobacter fecalis, Escherichia coli and Bacillus cereus. The MIC valauesagainst bacteria 50 ìgml-1. It was found that metanol and water extracts of S. virgaurea show antioxidant activity. It has been reported that there is an inverse relationship between dietary intake ofantioxidant-rich foods and the incidence of a number of human diseases, therefore these results are interesting. This plant, which may contain both polar and apolar antioxidant compounds, could be apotential source of natural antioxidants