Temperature Effects on Expression Levels of hsp Genes in Eggs and Second-Stage Juveniles of Meloidogyne hapla Chitwood, 1949.

Meloidogyne hapla is one of the most important nematode pathogens. It is a sedentary, biotrophic parasite of plants that overwinters in the soil or in diseased roots. The development of M. hapla is temperature dependent. Numerous studies have been performed on the effect of temperature on the development of M. hapla, but only a few of them analyzed the heat shock protein (hsp) genes. The aim of the study was to perform expression profiling of eight hsp genes (Mh-hsp90, Mh-hsp1, Mh-hsp4, Mh-hsp6, Mh-hsp60, Mh-dnj19, Mh-hsp43, and Mh-hsp12.2) at two development stages of M. hapla, i.e., in eggs and second-stage juveniles (J2). The eggs and J2 were incubated under cold stress (5 °C), heat stress (35 °C, 40 °C), and non-stress (10 °C, 20 °C, and 30 °C) conditions. Expression profiling was performed by qPCR. It was demonstrated that only two genes, Mh-hsp60 and Mh-dnj19, have been upregulated by heat and cold stress at both development stages. Heat stress upregulated the expression of more hsp genes than cold stress did. The level of upregulation of most hsp genes was more marked in J2 than in eggs. The obtained results suggest that the Mh-hsp90 and Mh-hsp1 genes can be used as bioindicators of environmental impacts on nematodes of the Meloidogyne genus.

Effect of Vicia sativa L. on Motility, Mortality and Expression Levels of hsp Genes in J2 Stage of Meloidogyne hapla.

Assuming that the seeds of Vicia sativa L. have a stressful effect on J2 stage Meloidogyne hapla, we undertook research on the effect of these seeds on the motility and mortality of J2 and determined the expression levels of selected hsp genes in J2. The assessment of the effect of V. sativa seeds on the motility of M. hapla specimens consisted of observing the movement of J2 immersed in a seed diffusate or in a tomato root filtrate at temperatures of 10, 17, and 21°C. In J2 treated with V. sativa (cv. Ina) seed diffusates, the expression level of hsp genes was determined by qPCR. J2 exposed to V. sativa diffusates were found to lose their motility, while their mortality did not exceed 30%. J2 in the seed diffusate were characterized by an increase in the expression levels of the Mh-hsp90, Mh-hsp1, and Mh-hsp43 genes. It is suggested that the hsp90 gene may be a potential bioindicator of the environmental impact on Meloidogyne nematodes. The impaired ability to move in J2 of M. hapla is attributable to the occurrence of V. sativa seeds in their habitat. These studies may contribute to developing methods of reducing crop damage caused by M. hapla.

Descriptions of two new and one known species of Parkellus Jairajpuri, Tahseen and Choi, 2001 (Nematoda: Mononchidae) and their phylogenetic position among Mononchida.

Two new species of Parkellus (Jairajpuri et al., 2001) from Vietnam and a population of Parkellus zschokkei (Ahmad and Jairajpuri, 2010; Menzel, 1913) from Ukraine are described, illustrated and their phylogenetic position among the Mononchida is presented. The molecular data (18S and 28S rDNA) are given for the three investigated species - first time for the genus Parkellus. Parkellus hagiangensis sp. nov. is characterized by a medium-sized buccal cavity, posterior position of the dorsal tooth located below the beginning of the pharynx, males having the ventromedian cuticular pores above and below the excretory pore, short spicules with conical proximal part; females with very faint pars refringens vaginae and small teardrop-shaped pieces, short pars distalis vaginae, the presence of small ventromedian vulval papillae. Parkellus tuyenquangensis sp. nov. is characterized by a medium-sized buccal cavity, posterior position of the dorsal tooth located above the beginning of the pharynx, males having the ventromedian cuticular pores above and below the excretory pore, medium-sized spicules with a cylindrical proximal part, very short lateral guiding pieces, females with very strongly sclerotized pars refringens vaginae, medium size teardrop-shaped pieces, short pars distalis vaginae thickened at the junction with pars refringens vaginae. The newly described species are morphologically most similar to P. parkus and P. zschokkei. An identification key to Parkellus species is presented.

Morphological and molecular characterisation of Tripylina gorganensis from the Slovak Republic as a contribution to the redescription of the species.

Specimens of Tripylina gorganensis, collected from a natural beech forest in Slovak Republic, are described and illustrated. These nematodes were initially identified as an undescribed species, morphologically similar to Tripylina gorganensis described from Iran. An important feature distinguishing both species was the presence of post-vulval uterine sac (PUS) in specimens from Slovak Republic, which, according to the original description (Asghari et al., 2012), was absent in Tripylina gorganensis. However, a careful re-examination of type specimens performed in this study revealed that T. gorganensis also has the post-vulval uterine sac. Consequently, the findings of the morphological and molecular studies performed on the Slovak population and observations on the type material contribute to the redescription of T. gorganensis.

First record of the ectoparasitic nematode Amplimerlinius macrurus (Nematoda: Tylenchida) on the perennial grass Miscanthus × giganteus (Angiosperms: Poaceae) in Ukraine.

The growing interest in biomass production of Miscanthus × giganteus (M × g) (Poaceae) on agricultural and marginal lands has prompted researches to identify plant pathogens and diseases affecting this crop which has a great potential for production of biofuels and different bioproducts. A soil survey of nematodes in the M × g rhizosphere and a report on the collection of the plant-parasitic nematode Amplimerlinius macrurus (Belonolaimidae) were accomplished in two locations in Ukraine. It is known that this family of nematodes can reduce the root system and biomass of Poaceae family plants. Both molecular and morphological characters were used to identify the nematodes; measurements and photomicrographs of the species were presented. This is the first documentation and description of A. macrurus in Ukraine to the best of our knowledge. Further investigation is underway to confirm the pathogenicity of this species on perennial grasses plantations.

In silico structural study of random amino acid sequence proteins not present in nature.

The three-dimensional structures of a set of 'never born proteins' (NBP, random amino acid sequence proteins with no significant homology with known proteins) were predicted using two methods: Rosetta and the one based on the 'fuzzy-oil-drop' (FOD) model. More than 3000 different random amino acid sequences have been generated, filtered against the non redundant protein sequence data base, to remove sequences with significant homology with known proteins, and subjected to three-dimensional structure prediction. Comparison between Rosetta and FOD predictions allowed to select the ten top (highest structural similarity) and the ten bottom (the lowest structural similarity) structures from the ranking list organized according to the RMS-D value. The selected structures were taken for detailed analysis to define the scale of structural accordance and discrepancy between the two methods. The structural similarity measurements revealed discrepancies between structures generated on the basis of the two methods. Their potential biological function appeared to be quite different as well. The ten bottom structures appeared to be 'unfoldable' for the FOD model. Some aspects of the general characteristics of the NBPs are also discussed. The calculations were performed on the EUChinaGRID grid platform to test the performance of this infrastructure for massive protein structure predictions.

Never born proteins as a test case for ab initio protein structures prediction.

The number of natural proteins although large is significantly smaller than the theoretical number of proteins that can be obtained combining the 20 natural amino acids, the so-called "never born proteins" (NBPs). The study of the structure and properties of these proteins allows to investigate the sources of the natural proteins being of unique characteristics or special properties. However the structural study of NPBs can also been intended as an ideal test for evaluating the efficiency of software packages for the ab initio protein structure prediction. In this research, 10.000 three-dimensional structures of proteins of completely random sequence generated according to ROSETTA and FOD model were compared. The results show the limits of these software packages, but at the same time indicate that in many cases there is a significant agreement between the prediction obtained.