Aphids (Hemiptera: Aphidoidea) on cultivated and self-sown plants in Greece

The present work covers original information on aphids (Hemiptera: Aphidoidea) from Greece during 1995–2005. The individual aphid taxa were collected from their host plants and identified. The plant taxa were classified in two major categories: cultivated and self-sown. The cultivated ones were classified as: herbaceous, climbing and trees. The selfsown ones were classified as: annual herbaceous, annual or biennial herbaceous, biennial or perennial herbaceous, perennial herbaceous, shrubby and trees Two hundred twelve plant taxa were identified on which 105 aphid taxa were recorded. We report 391 plant taxa-aphid taxa associations from which, 190 are referred to cultivated and 201 to self-shown plant taxa. Aphis gossypii was found to infest the widest spectrum of cultivated plant taxa whereas Brachycaudus helichrysi was found to infest the widest spectrum of self-sown plant taxa. Myzus persicae was found to infest the widest spectrum of the total number of plant taxa. Information for several economically unimportant aphid taxa in the area are also presented.     

Organochlorine pesticides in Muraena helena L. 1758 from the Eastern Adriatic Sea

This work examines the bioaccumulated organochlorine compounds in Muraena helena to draw attention to this species as a potential bioindicator organism. The morays were caught in the East Adriatic Sea, Elaphite Islands, near Dubrovnik, Croatia (lat: 42°45′38.8″; long: 17°45′53.6″) at the same location in summer (August, 2009) and winter (January, 2010), at depths from 5 to 10 m. Nine fish were caught by longline hooks per each field trip (total in summer and winter, N = 18). No single fish was free of organochlorines (OC), but not all pesticides were present in every fish. The concentration level was: Endrin > ppDDE > Heptachlor epoxide > Heptachlor > Aldrine > Lindane > βHCH > δHCH > Endrin aldehyde). Endrin was the only pesticide approaching the maximum concentrations proposed by the European Union and Croatia (summer max. concentration = 14.75 μg kg^?1; winter max. concentration = 8.35 μg kg^?1). All other pesticides ranged from 0.1 to 0.7 μg kg^?1. Heptachlor was absent in winter and δ‐HCH and Endrin aldehyde in summer, while Lindane and pp‐DDE had higher (P ≤ 0.05) concentrations in summer. Other residues had similar seasonal concentration levels. The p‐DDT was similar as in other biota from the Adriatic or Mediterranean. HCH concentrations corresponded to those found in organisms from the Italian area of the Adriatic. The endocrine and reproductive disrupting potential of the detected OCs are bases for future studies. Results show that morays are a good bioindicator model, with slight interspecies and seasonal variability in OC bioaccumulation as a consequence of diverse food consumption.     

Prediction of Protein–Protein Interaction Sites in Sequences and 3D Structures by Random Forests

Identifying interaction sites in proteins provides important clues to the function of a protein and is becoming increasingly relevant in topics such as systems biology and drug discovery. Although there are numerous papers on the prediction of interaction sites using information derived from structure, there are only a few case reports on the prediction of interaction residues based solely on protein sequence. Here, a sliding window approach is combined with the Random Forests method to predict protein interaction sites using (i) a combination of sequence- and structure-derived parameters and (ii) sequence information alone. For sequence-based prediction we achieved a precision of 84% with a 26% recall and an F-measure of 40%. When combined with structural information, the prediction performance increases to a precision of 76% and a recall of 38% with an F-measure of 51%. We also present an attempt to rationalize the sliding window size and demonstrate that a nine-residue window is the most suitable for predictor construction. Finally, we demonstrate the applicability of our prediction methods by modeling the Ras–Raf complex using predicted interaction sites as target binding interfaces. Our results suggest that it is possible to predict protein interaction sites with quite a high accuracy using only sequence information.     

Does allometry account for shape variability in <Emphasis Type="Italic">Ephedrus persicae</Emphasis> Froggatt (Hymenoptera: Braconidae: Aphidiinae) parasitic wasps?

We analysed linear measurements on various parts of the body and the configuration of 11 landmarks on the wing in a large sample of Ephedrus persicae that had emerged from 13 aphid host species, to assess whether static allometry (a measure of the scaling relationship between traits in a population of individuals at the same ontogenetic stage) accounts for variation in body shape. The analysed specimens came from several localities in Europe, Asia Minor, Japan and South America, and cover a large portion of the distribution area of E. persicae. We found that allometry accounts for variation in body shape among different biotypes within the E. persicae group. The allometric slopes for head size (HD), petiolus width (PETW), mesoscutum width (MSC), and ovipositor sheath length (OVPL) diverged significantly among biotypes, indicating biotype-specific allometries. The analysis of allometric variation in wing shape showed that the pattern and direction of allometric changes also differed among individuals that had emerged from different hosts. Our results (observed divergences in the directions of allometric slopes of particular morphometric traits and wing shape) suggest that allometric relations within E. persicae are not conserved, so that allometry itself changes, evolving differently in aphid parasitoids that emerge from different hosts.     

SW#db: GPU-Accelerated Exact Sequence Similarity Database Search

In recent years we have witnessed a growth in sequencing yield, the number of samples sequenced, and as a result–the growth of publicly maintained sequence databases. The increase of data present all around has put high requirements on protein similarity search algorithms with two ever-opposite goals: how to keep the running times acceptable while maintaining a high-enough level of sensitivity. The most time consuming step of similarity search are the local alignments between query and database sequences. This step is usually performed using exact local alignment algorithms such as Smith-Waterman. Due to its quadratic time complexity, alignments of a query to the whole database are usually too slow. Therefore, the majority of the protein similarity search methods prior to doing the exact local alignment apply heuristics to reduce the number of possible candidate sequences in the database. However, there is still a need for the alignment of a query sequence to a reduced database. In this paper we present the SW#db tool and a library for fast exact similarity search. Although its running times, as a standalone tool, are comparable to the running times of BLAST, it is primarily intended to be used for exact local alignment phase in which the database of sequences has already been reduced. It uses both GPU and CPU parallelization and was 4–5 times faster than SSEARCH, 6–25 times faster than CUDASW++ and more than 20 times faster than SSW at the time of writing, using multiple queries on Swiss-prot and Uniref90 databases     

3D Texture Analysis Reveals Imperceptible MRI Textural Alterations in the Thalamus and Putamen in Progressive Myoclonic Epilepsy Type 1, EPM1

Progressive myoclonic epilepsy type 1 (EPM1) is an autosomal recessively inherited neurodegenerative disorder characterized by young onset age, myoclonus and tonic-clonic epileptic seizures. At the time of diagnosis, the visual assessment of the brain MRI is usually normal, with no major changes found later. Therefore, we utilized texture analysis (TA) to characterize and classify the underlying properties of the affected brain tissue by means of 3D texture features. Sixteen genetically verified patients with EPM1 and 16 healthy controls were included in the study. TA was performed upon 3D volumes of interest that were placed bilaterally in the thalamus, amygdala, hippocampus, caudate nucleus and putamen. Compared to the healthy controls, EPM1 patients had significant textural differences especially in the thalamus and right putamen. The most significantly differing texture features included parameters that measure the complexity and heterogeneity of the tissue, such as the co-occurrence matrix-based entropy and angular second moment, and also the run-length matrix-based parameters of gray-level non-uniformity, short run emphasis and long run emphasis. This study demonstrates the usability of 3D TA for extracting additional information from MR images. Textural alterations which suggest complex, coarse and heterogeneous appearance were found bilaterally in the thalamus, supporting the previous literature on thalamic pathology in EPM1. The observed putamenal involvement is a novel finding. Our results encourage further studies on the clinical applications, feasibility, reproducibility and reliability of 3D TA.     

Fatty acid profiles of Trachinus radiatus Cuvier, 1829 (Perciformes‐Trachinoidei,Trachinidae)

The goal of this study was to analyse the fatty acid (FA) profiles of the streaked (starry) weever (Trachinus radiatus), a prized food fish in the countries of its distribution. Fish (N = 20) were sampled in July 2011. Location: 42.761019°N, 17.765090°W; Adriatic Sea, Elaphite Islands near Dubrovnik, Croatia, at 5–10 m depth using longline hooks; body length ranges: 24.1–47.2 cm, weight ranges: 120–960 g. Morphological species determination was genetically confirmed (Folmer region of COI gene). Biochemical analysis of T. radiatus muscular tissue (filet) revealed average ± SD dry matter of 252.3 ± 14.8 g/kg w.w.; moisture of 747.7 ± 14.8 g/kg w.w., and ash of 28.0 ± 6.9 g/kg w.w. Intramuscular crude protein content exceeded the total lipid (TL = 11.9 ± 4.0 g/kg w.w.) content approximately 17.7 fold. Unsaturated FA (UFA) was higher than saturated FA (SFA), with a predominance of polyunsaturated FA (PUFA). The ω3:ω6 ratio was 4.9:1, respectively. Among individually determined fatty acids, the PUFA 22:6n3 (DHA) was highly present (29.99 ± 2.75% TL) followed by a relatively high 20:5n3 (EPA) content. There was 25 fold higher EPA content than of substrate αLNA, and a 15.5 fold higher DHA content to DPAn3. Such ratios indicate that besides trophic ingestion, FA bioconversion elongase/desaturase synthesis pathways toward ω3 PUFA in Weevers could be highly efficient.     

Mitochondrial DNA Sequence and Phylogenetic Evaluation of Geographically Disparate Sus scrofa Breeds

Next generation sequencing of mitochondrial DNA (mtDNA) facilitates studies into the metabolic characteristics of production animals and their relation to production traits. Sequence analysis of mtDNA from pure-bred swine with highly disparate production characteristics (Mangalica Blonde, Mangalica Swallow-bellied, Meishan, Turopolje, and Yorkshire) was initiated to evaluate the influence of mtDNA polymorphisms on mitochondrial function. Herein, we report the complete mtDNA sequences of five Sus scrofa breeds and evaluate their position within the phylogeny of domestic swine. Phenotypic traits of Yorkshire, Mangalica Blonde, and Swallow-belly swine are presented to demonstrate their metabolic characteristics. Our data support the division of European and Asian breeds noted previously and confirm European ancestry of Mangalica and Turopolje breeds. Furthermore, mtDNA differences between breeds suggest function-altering changes in proteins involved in oxidative phosphorylation such as ATP synthase 6 (MT-ATP6), cytochrome oxidase I (MT-CO1), cytochrome oxidase III (MT-CO3), and cytochrome b (MT-CYB), supporting the hypothesis that mtDNA polymorphisms contribute to differences in metabolic traits between swine breeds. Our sequence data form the basis for future research into the roles of mtDNA in determining production traits in domestic animals. Additionally, such studies should provide insight into how mtDNA haplotype influences the extreme adiposity observed in Mangalica breeds.     

Interactive effects of elevated ozone and springtime frost on growth and physiology of birch (<Emphasis Type="Italic">Betula pendula</Emphasis>) in field conditions

We studied the impact of ozone enrichment and late frost, singly and interactively, on four birch (Betula pendula Roth) families selected from a naturally regenerated birch stand in southeastern Finland. Seedlings were exposed to 1.5× ambient ozone over one and a half growing seasons using free-air ozone enrichment system. Simulated springtime frost was implemented at the beginning of the second study year, 4 weeks after the bud burst. Plants were measured for timing of bud burst, visible ozone injuries, chlorophyll fluorescence, net photosynthesis and concentrations of photosynthetic pigments, as well as for growth and carbon allocation. Frost treatment caused a rapid 60% decline in net photosynthesis. The recovery of net photosynthesis from acute frost treatment was not complete during the subsequent 3 weeks, which led to significant growth reductions, decreased shoot/root ratio and accumulation of excess nitrogen in the leaves. Photosynthetic responses to ozone were very variable and family-specific. Concentrations of photosynthetic pigments were sensitive to both stress factors, while the maximum quantum yield of PSII was unaffected. Ozone exacerbated the effect of frost only on diameter increment. However, ozone and frost affected different seedling characters, e.g., ozone reduced pigments and frost collapsed net photosynthesis, and these effect combined appear to damage birch seedlings more than a single stress situation.