Immunological characterization of the Campylobacter jejuni 72Dz/92 cjaD gene product and its fusion with B subunit of E. coli LT toxin

Campylobacter jejuni 72Dz/92 cjaD gene, orthologue of C. jejuni NCTC 11168 cj0113, C. jejuni M275 omp18 and C. jejuni ATCC 29428 omp18, has been cloned, sequenced and analysed from the viewpoint of its immunological attributes. Neither the 5' nor 3' fragment of the cjaD encodes protein capable of reacting with anti-Campylobacter antibodies. Several fusions of the cjaD with eltB, which encodes B subunit of the E. coli LT toxin, have been constructed. The hybrid proteins, which differ in respect to their cellular localization, retain the ability to react with GM1 and are recognized by the antibodies specific for both moieties of the proteins. The fusion protein equipped with signal sequence, reveals a stronger affinity to GM1 than its equivalent which is unable to cross the inner membrane. Two recombinant plasmids (pUWM405 expressing both LTB and CjaD proteins and pUWM299 containing cjaD gene fused into 3' end of Escherichia coli eltB gene lacking signal sequence) were introduced into avirulent Salmonella enterica serovar Typhimurium strain where they are stably maintained.     

PSP_MCSVM: brainstorming consensus prediction of protein secondary structures using two-stage multiclass support vector machines

Secondary structure prediction is a crucial task for understanding the variety of protein structures and performed biological functions. Prediction of secondary structures for new proteins using their amino acid sequences is of fundamental importance in bioinformatics. We propose a novel technique to predict protein secondary structures based on position-specific scoring matrices (PSSMs) and physico-chemical properties of amino acids. It is a two stage approach involving multiclass support vector machines (SVMs) as classifiers for three different structural conformations, viz., helix, sheet and coil. In the first stage, PSSMs obtained from PSI-BLAST and five specially selected physicochemical properties of amino acids are fed into SVMs as features for sequence-to-structure prediction. Confidence values for forming helix, sheet and coil that are obtained from the first stage SVM are then used in the second stage SVM for performing structure-to-structure prediction. The two-stage cascaded classifiers (PSP_MCSVM) are trained with proteins from RS126 dataset. The classifiers are finally tested on target proteins of critical assessment of protein structure prediction experiment-9 (CASP9). PSP_MCSVM with brainstorming consensus procedure performs better than the prediction servers like Predator, DSC, SIMPA96, for randomly selected proteins from CASP9 targets. The overall performance is found to be comparable with the current state-of-the art. PSP_MCSVM source code, train-test datasets and supplementary files are available freely in public domain at: and     

Mesostigmatic mites (Acari: Mesostigmata) in nests of the Eurasian griffon vulture (<Emphasis Type="Italic">Gyps fulvus</Emphasis>) in Croatia

We examined the species composition and community structure of mites of the order Mesostigmata (Acari) in nests of the Eurasian griffon vulture (Gyps fulvus Hablizl, 1783) in Croatia. Material collected from 18 nests included 565 mites belonging to seven species. The most abundant species were Leiodinychus orbicularis (C.L. Koch, 1839) (Trematuridae) and Androlaelaps casalis (Berlese, 1887) (Laelapidae). The results were compared with the community structure and frequency of dominant species of Mesostigmata in nests of 32 other bird species. Leiodinychus orbicularis occurred in the nests of 13 species of birds. It is a typical nidicolous species which occurs most frequently in the perennial nests of birds of prey. In contrast, A. casalis rarely occurs in the nests of birds of prey.     

Indirect Short- and Long-Term Effects of Aboveground Invertebrate and Vertebrate Herbivores on Soil Microarthropod Communities

Recognition is growing that besides ungulates, small vertebrate and invertebrate herbivores are important drivers of grassland functioning. Even though soil microarthropods play key roles in several soil processes, effects of herbivores—especially those of smaller body size—on their communities are not well understood. Therefore, we progressively excluded large, medium and small vertebrate and invertebrate herbivores for three growing seasons using size-selective fences in two vegetation types in subalpine grasslands; short-grass and tall-grass vegetation generated by high and low historical levels of ungulate grazing. Herbivore exclusions generally had few effects on microarthropod communities, but exclusion of all herbivore groups resulted in decreased total springtail and Poduromorpha richness compared with exclusion of only ungulates and medium-sized mammals, regardless of vegetation type. The tall-grass vegetation had a higher total springtail richness and mesostigmatid mite abundance than the short-grass vegetation and a different oribatid mite community composition. Although several biotic and abiotic variables differed between the exclusion treatments and vegetation types, effects on soil microarthropods were best explained by differences in nutrient and fibre content of the previous year’s vegetation, a proxy for litter quality, and to a lesser extent soil temperature. After three growing seasons, smaller herbivores had a stronger impact on these functionally important soil microarthropod communities than large herbivores. Over longer time-scales, however, large grazers created two different vegetation types and thereby influenced microarthropod communities bottom-up, e.g. by altering resource quality. Hence, both short- and long-term consequences of herbivory affected the structure of the soil microarthropod community.     

Quantification of Alternaria,Cladosporium, Fusarium and Penicillium verrucosum in Conventional and Organic Grains by qPCR

We analysed the levels of Alternaria, Cladosporium, Fusarium and Penicillium verrucosum in grain samples harvested in 2011 and 2012 from conventional and organic farms using qPCR. In general, both Alternaria and Cladosporium occurred in all cereal grains in the highest quantities, followed by P. verrucosum and Fusarium. Alternaria, Cladosporium and P. verrucosum had the highest levels in crop mixtures, barley and rye and lower levels in wheat, while Fusarium levels were the highest in crop mixtures and wheat. The levels of Alternaria and P. verrucosum were higher in organic rye and wheat than conventional grains. Although the level of Fusarium was higher in conventional than organic rye, opposite results were obtained for crop mixtures. A positive correlation was found between Alternaria, Cladosporium and P. verrucosum, indicating that similar factors might affect the distribution of these fungi in grains.     

Notes on the genus Quekettia (Orchidaceae) with descriptions of two new species from Colombia and Guyana

Two new species of the orchid genus Quekettia are described. Colombian Quekettia aureliae is distinguished from similar Q. microscopica by the pandurate lip with a pair of small, flap‐like calli in the isthmus between hypo‐ and epichile, and deeply emarginated epichile apex. Quekettia senghasiana found in Guyana resembles Q. papillosa but it is characterized by the free lateral sepals, oblanceolate, obtuse petals and much larger lip which is oblong–obovate in outline and with lip disc being papillate only near the base.     

Predation-mediated coexistence of large- and small-bodied Daphnia at different food levels

Using an individual-based age-structured population model (a combination of O'Brien's apparent-prey-size approach, Eggers's reactive-field-volume model, and Holling's disk equation), we could predict that (1) a Daphnia population could be kept at low density by fish predation irrespective of food level, with greater recruitment at higher food being instantly compensated for by raised mortality reflecting increased predation, and (2) Daphnia density levels are species specific and inversely related to both body size at first reproduction and the reaction distance at which a foraging fish sees its Daphnia prey. These two hypotheses were experimentally tested in outdoor mesocosms with two Daphnia species of different body sizes grown in the absence or presence of fish that were allowed to feed for 2-3 h each evening. While each Daphnia quickly reached high density with reproduction halted by food limitation in the absence of fish, the populations stayed at much lower species-specific density levels, similar in low and high food concentrations, in the presence of fish. This suggests that our model offers a reasonable mechanistic explanation for the coexistence of large- and small-bodied zooplankton in proportions reflecting their body sizes throughout habitats comprising a wide productivity spectrum, with each species at a density level at which it becomes included in a predator's diet.     

Ultrastructural changes in the developing chicken cornea following caffeine administration

Caffeine is one of the most frequently consumed psychoactive substances. It has been known for many years that caffeine at high concentrations exerts harmful effects on both women's and laboratory animals' fertility, moreover it may impair normal development of many organs in the prenatal period. So far there have been few studies performed that demonstrate teratogenic effects of caffeine on structures of the developing eye, particularly the cornea. The aim of the study was to show ultrastructural changes in the developing cornea, as the effect of caffeine administration to chicken embryos. The experimental materials were 26 chicken embryos from incubated breeding eggs. Eggs were divided into two groups: control (n=30) in which Ringer liquid was administrated, and experimental (n=30) in which teratogenic dose of caffeine 3.5mg/egg was given. In 36th hour of incubation solutions were given with cannula through hole in an egg shell directly onto amniotic membrane. After closing the hole with a glass plate and paraffine, eggs were put back to incubator. In 10th and 19th day of incubation corneas were taken for morphological analysis with a use of electron microscopy. Administration of caffeine during chicken development causes changes of collagen fibers of Bowman's membrane patterns and of the corneal stroma but it also changes proportion of amount of collagen fibers and of the stromal cells.