Knowledge-based computational methods for identifying or designing novel,non-homologous antimicrobial peptides

We describe computational approaches for identifying promising lead candidates for the development of peptide antibiotics, in the context of quantitative structure–activity relationships (QSAR) studies for this type of molecule. A first approach deals with predicting the selectivity properties of generated antimicrobial peptide sequences in terms of measured therapeutic indices (TI) for known antimicrobial peptides (AMPs). Based on a training set of anuran AMPs, the concept of sequence moments was used to construct algorithms that could predict TIs for a second test set of natural AMPs and could also predict the effect of point mutations on TI values. This approach was then used to design peptide antibiotics (adepantins) not homologous to known natural or synthetic AMPs. In a second approach, many novel putative AMPs were identified from DNA sequences in EST databases, using the observation that, as a rule, specific subclasses of highly conserved signal peptides are associated exclusively with AMPs. Both anuran and teleost sequences were used to elucidate this observation and its implications. The predicted therapeutic indices of identified sequences could then be used to identify new types of selective putative AMPs for future experimental verification.     

Stomata in some species of genus <Emphasis Type="Italic">Arum</Emphasis> from the Eastern Slavonia and Baranya region

Types and the number of stomata in the following Arum species: Arum italicum Mill., Arum maculatum var. maculatum L. and Arum maculatum var. immaculatum L., Arum alpinum var. pannonicum Terpo. and Arum alpinum var. intermedium Schur. in three different locations in Zablaće, Normanci and Bilje were investigated. The most prevalent stomata type at both upper and lower epidermis for each Arum species was mostly stomata type paracytic, followed by hexacytic, tetracytic or brachyparacytic as far as locality is concerned. Helicocytic type was more prevalent in Arum alpinum var. pannonicum Terpo. and Arum alpinum var. intermedium Schur. at Bilje. Other stomata types were very rare. A striking regularity in the occurrence of stomata types was not found within a single species. Some stomata types, however, were found either at adaxial or abaxial epidermis or were not present at all. The number of stomata per square mm varied from 25 to 651. A statistically significant difference in the number of stomata per square mm at upper and lower epidermis among Arum species was determined in locations Zablaće and Normanci, whereas no statistically significant differences were found in location Bilje.     

First international external quality assessment of molecular detection of Crimean-Congo hemorrhagic fever virus

Crimean-Congo hemorrhagic fever (CCHF) is a zoonosis caused by a Nairovirus of the family Bunyaviridae. Infection is transmitted to humans mostly by Hyalomma ticks and also by direct contact with the blood or tissues of infected humans or viremic livestock. Clinical features usually include a rapid progression characterized by hemorrhage, myalgia and fever, with a lethality rate up to 30%. CCHF is one of the most widely distributed viral hemorrhagic fevers and has been reported in Africa, the Middle East and Asia, as well as parts of Europe. There is no approved vaccine or specific treatment against CCHF virus (CCHFV) infections. In this context, an accurate diagnosis as well as a reliable surveillance of CCHFV infections is essential. Diagnostic techniques include virus culture, serology and molecular methods, which are now increasingly used. The European Network for the Diagnostics of "Imported" Viral Diseases organized the first international external quality assessment of CCHVF molecular diagnostics in 2011 to assess the efficiency and accurateness of CCHFV molecular methods applied by expert laboratories. A proficiency test panel of 15 samples was distributed to the participants including 10 different CCHFV preparations generated from infected cell cultures, a preparation of plasmid cloned with the nucleoprotein of CCHFV, two CCHFV RNA preparations and two negative controls. Forty-four laboratories worldwide participated in the EQA study and 53 data sets were received. Twenty data sets (38%) met all criteria with optimal performance, 10 (19%) with acceptable performance, while 23 (43%) reported results showing a need for improvement. Differences in performance depended on the method used, the type of strain tested, the concentration of the sample tested and the laboratory performing the test. These results indicate that there is still a need for improving testing conditions and standardizing protocols for the molecular detection of Crimean-Congo hemorrhagic fever virus.     

Diversity and Biotic Homogenization of Urban Land-Snail Faunas in Relation to Habitat Types and Macroclimate in 32 Central European Cities

The effects of non-native species invasions on community diversity and biotic homogenization have been described for various taxa in urban environments, but not for land snails. Here we relate the diversity of native and non-native land-snail urban faunas to urban habitat types and macroclimate, and analyse homogenization effects of non-native species across cities and within the main urban habitat types. Land-snail species were recorded in seven 1-ha plots in 32 cities of ten countries of Central Europe and Benelux (224 plots in total). Each plot represented one urban habitat type characterized by different management and a specific disturbance regime. For each plot, we obtained January, July and mean annual temperature and annual precipitation. Snail species were classified into either native or non-native. The effects of habitat type and macroclimate on the number of native and non-native species were analysed using generalized estimating equations; the homogenization effect of non-native species based on the Jaccard similarity index and homogenization index. We recorded 67 native and 20 non-native species. Besides being more numerous, native species also had much higher beta diversity than non-natives. There were significant differences between the studied habitat types in the numbers of native and non-native species, both of which decreased from less to heavily urbanized habitats. Macroclimate was more important for the number of non-native than native species; however in both cases the effect of climate on diversity was overridden by the effect of urban habitat type. This is the first study on urban land snails documenting that non-native land-snail species significantly contribute to homogenization among whole cities, but both the homogenization and diversification effects occur when individual habitat types are compared among cities. This indicates that the spread of non-native snail species may cause biotic homogenization, but it depends on scale and habitat type.     

Alburnoides manyasensis (Actinopterygii,?Cyprinidae), a new species of cyprinid fish from?Manyas?Lake?basin,?Turkey

Alburnoides manyasensis, sp. n., is described from the Koca Stream (Lake Manyas drainage, Marmara Sea basin) in Anatolia. It is distinguished from all species of Alburnoides in Turkey and adjacent regions, Alburnoides tzanevi (Rezovska [Rezve], Istranca and Terkos streams in the western Black Sea drainage), Alburnoides cf. smyrnae (Banaz Stream, a drainage of Büyük Menderes River, Aegean Sea basin), Alburnoides fasciatus (streams and rivers in the eastern Black Sea drainage) and Alburnoides eichwaldii (Kura and Aras rivers [a drainage of Kura River], Caspian Sea basin) by a combination of the following characters (none unique to the species):marked hump at nape, especially in specimens larger than 60 mm SL; partly developed ventral keel between pelvic fin and anal fin, scaleless 1/2 to 2/3 its length; body depth at dorsal-fin origin 29−32% SL; caudal peduncle depth 11−12% SL; 45–52+ 2–3 lateral-line scales; 9–12 scale rows between lateral line and dorsal-fin origin; 4–5 scale rows between lateral line and anal-fin origin, 10½–12½ branched anal-fin rays; 40–42 total vertebrae.     

Effect of Lycopene Application in Rats with Experimental Diabetes Using Lipoprotein, Paraoxonase and Cytokines

This study was conducted with the purpose of researching the effect of lycopene application on lipoprotein, paraoxonase (PON) and cytokines that are projected to be used in the diagnosis and treatment of diabetes by making experimental diabetes. At the end of a 1-month trial period, under ether anesthesia with jelly tubes, blood samples were taken from rat hearts. Blood samples were centrifuged and serum was obtained. From the serum samples, HbA_1c, paraoxonase activity, lipoprotein levels and cytokines were determined. HbA_1c levels and PON activity were found to be p < 0.001. At the triglyceride level, with regard to the control group, in all the groups a significant rise occurred (p ≤ 0.001). At the cholesterol level, with regard to the control group, a decline was observed in the other groups (p < 0.05). At the VLDL level, with regard to the control group, a significant rise was observed in the other groups (p < 0.05). At the HDL (p < 0.001) and LDL (p < 0.05) levels, with regard to the control group, a significant decline was observed in the other groups. At the TNF-α, IL-2, IL-6 and IL-10 levels no difference was found (p > 0.05). Experimental diabetes models have an important place in analyzing diabetes complications and determining treatment approaches.     

Alien invasive neophytes of the Southeastern part of the Pannonian Plain

Floristic diversity in the Pannonian Plain is the result of mosaic habitat composition, characterized by steppes, saline meadows, and lowland forests along major rivers. In the last few centuries, the flora has become enriched by species introduced by human activities, such as colonization and industrialization. Presently it consists of nearly 1800 species. As a result of 30 years of field research as well as herbarium and literature searches, a list of invasive alien neophytes has been compiled and is presented here. The list includes 152 species, classified as either naturalized, casual, or unknown. One of the species is listed in Red Book of Serbian Flora. Eighty species are naturalized, and 61 are casual species. The majority of the introduced flora originates from North America (66) and the Old World (43). Most alien invasive species of the Southeastern part of the Pannonian Plain, were introduced accidentally by seed material or deliberately by nursery saplings. The annual and perennial herbaceous plants, which flower in the summer and summer-autumn periods, are represented in the greatest numbers. The alien flora was further analyzed with respect to taxonomy, life forms, pollination, and seed dispersal mode. The greatest number of alien species appears in anthropogenic and semi-natural habitats (59). In natural habitats, 45 invasive taxa were recorded, representing a conservation threat to biodiversity.