Dimitar Dimitrov

Bridging onshore and offshore present‐day kinematics of central and eastern Mediterranean: Implications for crustal dynamics and mantle flow

We present a new kinematic and strain model of an area encompassing the Calabrian and Hellenic subduction zones, western Anatolia and the Balkans. Using Haines and Holts (1993) method, we derive continuous velocity and strain rate fields by interpolating geodetic velocities, including recent GPS data in the Balkans. Relative motion between stable Eurasia and the western Aegean Sea is gradually accommodated by distributed N-S extension from Southern Balkans to the Eastern Corinth Gulf, so that the westward propagation of the North Anatolian Fault (NAF) throughout continental Greece or Peloponnesus is not required. We thus propose that the NAF terminates in north Aegean and that N-S extension localized in the Corinth Gulf and distributed in Southern Balkans is due to the retreat of the Hellenic slab. The motion of the Hyblean plateau, Apulia Peninsula, south Adriatic Sea, Ionian Basin and Sirte plain can be minimized by a single rigid rotation around a pole located in the Sirte plain, compatible with the opening the Pelagian rifts (2–2.5 mm/yr) and seismotectonics in Libya. We interpret the trenchward ultraslow motion of the Calabrian arc (2–2.5 mm/yr) as pure collapse, the Calabrian subduction being now inactive. In the absolute plate motion reference frame, our modeled velocity field depicts two toroidal crustal patterns located at both ends of the Hellenic subduction zone, clockwise in NW Greece and counter-clockwise in western Anatolia. We suggest the NW Greece toroidal pattern is the surface expression of a slab tear and consequent toroidal asthenospheric flow.

Polymerase chain reaction-based identification of Plasmodium (Huffia) elongatum, with remarks on species identity of haemosporidian lineages deposited in GenBank

Numerous lineages of avian malaria parasites of the genus Plasmodium have been deposited in GenBank. However, only 11 morphospecies of Plasmodium have been linked to these lineages. Such linking is important because it provides opportunities to combine the existing knowledge of traditional parasitology with novel genetic information of these parasites obtained by molecular techniques. This study linked one mitochondrial cytochrome b (cyt b) gene lineage with morphospecies Plasmodium (Huffia) elongatum, a cosmopolitan avian malaria parasite which causes lethal disease in some birds. One species of Plasmodium (mitochondrial cyt b gene lineage P-GRW6) was isolated from naturally infected adult great reed warblers (Acrocephalus arundinaceus) and inoculated to one naive juvenile individual of the same host species. Heavy parasitaemia developed in the subinoculated bird, which enabled identification of the morphospecies and deposition of its voucher specimens. The parasite of this lineage belongs to P. elongatum. Illustrations of blood stages of this parasite are given. Other lineages closely related to P. elongatum were identified. The validity of the subgenus Huffia is supported by phylogenetic analysis. Mitochondrial cyt b gene lineages, with GenBank accession nos. AF069611 and AY733088, belong to Plasmodium cathemerium and P. elongatum, respectively; these lineages have been formerly attributed to P. elongatum and P. relictum, respectively. Some other incorrect species identifications of avian haematozoa in GenBank have been identified. We propose a strategy to minimise the number of such mistakes in GenBank in the future.

Genetic diversity of avian blood parasites in SE Europe: Cytochrome b lineages of the genera Plasmodium and Haemoproteus (Haemosporida) from Bulgaria

We used a nested PCR protocol to examine the genetic diversity of cytochrome b (cyt b) lineages from blood parasites of the genera Plasmodium and Haemoproteus in birds in Bulgaria. In total, 460 birds of 43 species and 14 families (mostly passerines) were examined for the presence of infections. Of them, 267 were recognised as infected with haemosporidian parasites. Mixed infections were recorded in 24 individuals (9%). Besides the 24 individuals with mix infections, 114 (43%) were positive for Plasmodium spp. and 129 (48%) for Haemoproteus spp. We identified 52 genetic lineages of haemosporidian parasites: 38 of Haemoproteus and 14 of Plasmodium. Twelve new cyt b lineages of Haemoproteus were recorded; they occurred in the following hosts: grey-faced woodpecker (Picus canus), golden oriole (Oriolus oriolus), jay (Garrulus glandarius), barred warbler (Sylvia nisoria), song thrush (Turdus philomelos), spotted flycatcher (Muscicapa striata), spanish sparrow (Passer hispaniolensis), hawfinch (Coccothraustes coccothraustes), and cirl bunting (Emberiza cirlus). We also detected 22 new host records for previously known lineages. The most common lineage was SGS1 (Plasmodium relictum), which had a total prevalence of 14% and occurred in 8 host species belonging to 5 families. Three of the cyt b lineages of genus Haemoproteus (DURB1, DURB2 and SYNIS2) showed more than 5% divergence from all described morphologically lineages. These lineages probably represent at least 2 different morphospecies which remains to be identified.

Molecular characterization of five widespread avian haemosporidian parasites (Haemosporida), with perspectives on the PCR-based detection of haemosporidians in wildlife

Haemosporidians (Haemosporida) are cosmopolitan in birds. Over 250 species of these blood parasites have been described and named; however, molecular markers remain unidentified for the great majority of them. This is unfortunate because linkage between DNA sequences and identifications based on morphological species can provide important information about patterns of transmission, virulence, and evolutionary biology of these organisms. There is an urgent need to remedy this because few experts possess the knowledge to identify haemosporidian species and few laboratories are involved in training these taxonomic skills. Here, we describe new mitochondrial cytochrome b markers for the polymerase chain reaction (PCR)-based detection of four widespread species of avian Haemoproteus (Haemoproteus hirundinis, Haemoproteus parabelopolskyi, Haemoproteus pastoris, Haemoproteus syrnii) and 1 species of Plasmodium (Plasmodium circumflexum). Illustrations of blood stages of the reported species are given, and morphological and phylogenetic analyses identify the DNA lineages that are associated with these parasites. This study indicates that morphological characters, which have been traditionally used in taxonomy of avian haemosporidian parasites, have a phylogenetic value. Perspectives on haemosporidian diagnostics using microscopic and PCR-based methods are discussed, particularly the difficulties in detection of light parasitemia, coinfections, and abortive parasite development. We emphasize that sensitive PCR amplifies more infections than can be transmitted; it should be used carefully in epidemiology studies, particularly in wildlife parasitology research. Because molecular studies are describing remarkably more parasite diversity than previously expected, the need for traditional taxonomy and traditional biological knowledge is becoming all the more crucial. The linkage of molecular and morphological approaches is worth more of the attention of researchers because this approach provides new knowledge for better understanding insufficiently investigated lethal diseases caused by haemosporidian infections, particularly on the exoerythrocytic (tissue) and vector stages. That requires close collaboration between researchers from different fields with a common interest.

A new development of the oasis computer system for modeling molecular properties

Abstract A description of the new version of the OASIS system for computer assisted quantitative structure-property analysis is presented. The newly developed system is much more flexible and versatile than the version recently introduced. The most significant changes are the amendments within the input module. The originally developed line notion system is described in detail. The routine for an exhaustive generation of all stereo, optical and torsional isomers should also be emphasized here. The input module provides a database management for a library with three-dimensional molecular models, including substructure search. The list of the calculated topological, steric and electronic indices is extended by physicochemical parameters such as partition coefficient, molecular refraction, van der Waals volume and surface, etc. The basic advantages of the system are delineated. Some numerical data on the performance of the improved OASIS method are presented.

A New Morphologically Distinct Avian Malaria Parasite That Fails Detection By Established Polymerase Chain Reaction–Based Protocols for Amplification of the Cytochrome B Gene

Abstract: Plasmodium polymorphum n. sp. (Haemosporida, Plasmodiidae) was found in the skylark, Alauda arvensis (Passeriformes: Alaudidae), during autumnal migration in southern Italy. This organism is illustrated and described based on the morphology of its blood stages. The most distinctive feature of this malaria parasite is the clear preference of its blood stages (trophozoites, meronts, and gametocytes) for immature red blood cells, including erythroblasts. Based on preference of erythrocytic meronts for immature red blood cells, P. polymorphum is most similar to species of the subgenus Huffia. This parasite can be readily distinguished from all other bird malaria parasites, including Plasmodium (Huffia) spp., due to preferential development and maturation of its gametocytes in immature red blood cells, a unique character for avian Plasmodium spp. In addition, the margins of nuclei in blood stages of P. polymorphum are markedly smooth and distinct; this is also a distinct diagnostic feature of this parasite. Plasmodium polymorphum has been recorded only in the skylark; it is probably a rare parasite, whose host range and geographical distribution remain unclear. Microscopic examination detected a light infection of Plasmodium relictum (lineage GRW11, parasitemia of <0.01%) in the same sample with P. polymorphum; the latter parasite clearly predominated (3.5% parasitemia). However, experienced researchers were unable to detect sequences of mitochondrial cytochrome b gene (cyt b) of P. polymorphum from the microscopically positive sample by using published and newly designed primers for DNA amplification of avian Plasmodium spp. The light parasitemia of P. relictum was easily detectable using several polymerase chain reaction (PCR)–based assays, but P. polymorphum was undetectable in all applied assays. Quantitative PCR also showed the presence of light parasitemia (0.06%) of the lineage GRW11 in this sample. This supports the conclusion that the morphologically distinct parasite observed along with P. relictum and predominant in the sample is genetically dissimilar from the lineage GRW11 based on cyt b sequence. In samples with co-infections, general PCR protocols tend to favor the amplification of the parasite with the higher parasitemia or the amplification with the best matching sequence to the primers. Because the parasitemia of P. polymorphum was >50-fold higher than that of P. relictum and several different primers were tested, we suggest that the failure to amplify P. polymorphum is a more complex problem than why co-infections are commonly overlooked in PCR-based studies. We suggest possible explanations of these results and call for additional research on evolution of mitochondrial genome of hemosporidian parasites.

Plasmodium spp.: An experimental study on vertebrate host susceptibility to avian malaria.

The interest in experimental studies on avian malaria caused by Plasmodium species has increased recently due to the need of direct information about host-parasite interactions. Numerous important issues (host susceptibility, development of infection, the resistance and tolerance to avian malaria) can be answered using experimental infections. However, specificity of genetically different lineages of malaria parasites and their isolates is largely unknown. This study reviews recent experimental studies and offers additional data about susceptibility of birds to several widespread cytochrome b (cyt b) lineages of Plasmodium species belonging to four subgenera. We exposed two domesticated avian hosts (canaries Serinus canaria and ducklings Anas platyrhynchos) and also 16 species of common wild European birds to malaria infections by intramuscular injection of infected blood and then tested them by microscopic examination and PCR-based methods. Our study confirms former field and experimental observations about low specificity and wide host-range of Plasmodium relictum (lineages SGS1 and GRW11) and P. circumflexum (lineage TURDUS1) belonging to the subgenera Haemamoeba and Giovannolaia, respectively. However, the specificity of different lineages and isolates of the same parasite lineage differed between species of exposed hosts. Several tested Novyella lineages were species specific, with a few cases of successful development in experimentally exposed birds. The majority of reported cases of mortality and high parasitaemia were observed during parasite co-infections. Canaries were susceptible mainly for the species of Haemamoeba and Giovannolaia, but were refractory to the majority of Novyella isolates. Ducklings were susceptible to three malaria infections (SGS1, TURDUS1 and COLL4), but parasitaemia was light (<0.01%) and transient in all exposed birds. This study provides novel information about susceptibility of avian hosts to a wide array of malaria parasite lineages, outlining directions for future experimental research on various aspects of biology and epidemiology of avian malaria.

Conformational Coverage by a Genetic Algorithm

A new approach for coverage of the conformational space by a limited number of conformers is proposed. Instead of using a systematic search whose time complexity increases exponentially with degrees of freedom, a genetic algorithm (GA) is employed to minimize 3D similarity among the conformers generated. This makes the problem computationally feasible even for large, flexible molecules. The 3D similarity of a pair of conformers is assumed to be reciprocal to the root-mean-square (rms) distance between identical atomic sites in an alignment providing its minimum. Thus, in contrast to traditional GA, the fitness of a conformer is not quantified individually but only in conjunction with the population it belongs to. The approach handles the following stereochemical and conformational degrees of freedom:  rotation around acyclic single and double bonds, inversion of stereocenters, flip of free corners in saturated rings, and reflection of pyramids on the junction of two or three saturated rings. The latter tw...

Two new species of Haemoproteus Kruse, 1890 (Haemosporida, Haemoproteidae) from European birds, with emphasis on DNA barcoding for detection of haemosporidians in wildlife

Two new species of Haemoproteus Kruse, 1890 (Haemosporida, Haemoproteidae) are described: Haemoproteus (Parahaemoproteus) homovelans n. sp. from Grey-faced Woodpecker, Picus canus Gmelin, and Haemoproteus (Parahaemoproteus) concavocentralis n. sp. recorded in Hawfinch, Coccothraustes coccothraustes (Linnaeus), both sampled in Bulgaria. The morphology of the gametocytes and their host-cells are described and mitochondrial cytochrome b (cyt b) gene sequences are generated. Haemoproteus homovelans possesses circumnuclear gametocytes lacking volutin granules. This parasite is particularly similar to Haemoproteus velans Coatney & Roudabush, 1937 also possessing circumnuclear gametocytes that are, however, overfilled with volutin. Haemoproteus concavocentralis can be readily distinguished from all described avian haemoproteids due to the presence of an unfilled concave space between the central part of advanced gametocytes and erythrocyte nucleus. Bayesian phylogenetic analyses of 40 haemosporidian cyt b lineages showed close relationships of H. concavocentralis (hHAWF2) with a group of Haemoproteus spp. possessing gametocytes that are pale-stained with Giemsa. The lineage hPICAN02 of H. homovelans clustered with parasites infecting non-passerine birds. Phylogenetic analyses support the current subgeneric classification of the avian haemoproteids and suggest that cyt b lineage hPIPUB01 (GenBank EU254552) has been incorrectly assigned to Haemoproteus picae Coatney & Roudabush, 1937, a common parasite of corvid birds (Passeriformes). This study emphasises the importance of combining molecular techniques and light microscopy in the identification and field studies of avian haemosporidian parasites. Future development of barcodes for molecular identification of haemoproteids will allow better diagnostics of these infections, particularly in veterinary studies addressing insufficiently investigated tissue pathology caused by these parasites.

Co‐infections and environmental conditions drive the distributions of blood parasites in wild birds

Experimental work increasingly suggests that non-random pathogen associations can affect the spread or severity of disease. Yet due to difficulties distinguishing and interpreting co-infections, evidence for the presence and directionality of pathogen co-occurrences in wildlife is rudimentary. We provide empirical evidence for pathogen co-occurrences by analysing infection matrices for avian malaria (Haemoproteus and Plasmodium spp.) and parasitic filarial nematodes (microfilariae) in wild birds (New Caledonian Zosterops spp.). Using visual and genus-specific molecular parasite screening, we identified high levels of co-infections that would have been missed using PCR alone. Avian malaria lineages were assigned to species level using morphological descriptions. We estimated parasite co-occurrence probabilities, while accounting for environmental predictors, in a hierarchical multivariate logistic regression. Co-infections occurred in 36% of infected birds. We identified both positively and negatively correlated parasite co-occurrence probabilities when accounting for host, habitat and island effects. Two of three pairwise avian malaria co-occurrences were strongly negative, despite each malaria parasite occurring across all islands and habitats. Birds with microfilariae had elevated heterophil to lymphocyte ratios and were all co-infected with avian malaria, consistent with evidence that host immune modulation by parasitic nematodes facilitates malaria co-infections. Importantly, co-occurrence patterns with microfilariae varied in direction among avian malaria species; two malaria parasites correlated positively but a third correlated negatively with microfilariae. We show that wildlife co-infections are frequent, possibly affecting infection rates through competition or facilitation. We argue that combining multiple diagnostic screening methods with multivariate logistic regression offers a platform to disentangle impacts of environmental factors and parasite co-occurrences on wildlife disease.