New radiolarian genera and species from the Lower Permian of the Southern Urals and Northern Mugodzhary

Two new genera and five new species of Lower Permian radiolarians, Arcoclathrata alekseevi gen. et sp. nov., Entactinia pinrasensis sp. nov., Microporosa rozhnovi gen. et sp. nov., M. aktastensis sp. nov., and Somphoentactinia saecularis sp. nov., from the Southern Urals and Northern Mugodzhary are described. The new spherical radiolarian taxa belong to three orders: Entactiniata, Cancelliata, and Spongiata of two classes, Sphaerellaria and Spumellaria.     

DNA analysis reveals rich diversity of <Emphasis Type="Italic">Hydnotrya</Emphasis> with emphasis on the species found in China

Molecular analysis of the truffle genus Hydnotrya was conducted with nrDNA-ITS sequences available including newly generated sequences from Chinese specimens. Twenty-one phylotypes were recognized with the threshold of 97% ITS identity. Seven phylotypes corresponded to the described species, H. bailii, H. cerebriformis, H. cubispora, H. laojunshanensis, H. michaelis, H. cf. variiformis, and H. tulasnei, and four phylotypes represented by Chinese specimens were described and illustrated as new species, i.e., H. badia, H. brunneospora, H. nigricans, and H. puberula. The remaining ten phylotypes may represent undescribed species. Moreover, the 21 phylotypes grouped into four distinct clades each having as core species H. cerebriformis, H. cubispora, H. michaelis, and H. tulasnei, respectively, which were strongly supported by phylogenetic analysis and morphological characterization.     

New Zealand Eocene,Oligocene and Miocene Macrofossil and Pollen Records and Modern Plant Distributions in the Southern Hemisphere

The modern New Zealand flora has a relatively low number of families and genera in relation to land area, but well-preserved macrofossils and pollen from three sites in southern New Zealand suggest that the floras in Eocene, Oligocene and Miocene times were much more diverse at the generic level. At Pikopiko, Southland, a late Eocene in situ forest with fern understory was dominated by conifers, Casuarinaceae, Lauraceae, Nothofagus, Proteaceae, and mesothermal angiosperms including palms (aff. Calamus), Sapindaceae: Cupaniae and Picrodendraceae. At Newvale Mine, Southland, a leaf bed within a thick lignite seam represents leaf fossils preserved in a late Oligocene oligotrophic bog. This site demonstrates that Agathis, Dacrycarpus, Dacrydium, Halocarpus, Microcachrys, Podocarpus and Phyllocladus coexisted with diverse angiosperms including Nothofagus, Gymnostoma, Cunoniaceae, Ericaceae, Sapindaceae and several Proteaceae. Pollen data add Meliaceae, Myrtaceae, Onagraceae and Rubiaceae to the flora. At Foulden Maar, Otago, mummified leaves and flowers, including several with in situ pollen, demonstrate the existence of a diverse flora surrounding an Early Miocene lake. This site contains numerous monocot macrofossils including Astelia, Cordyline, Ripogonum and Typha, as well as the oldest fossils known for Orchidaceae and Luzuriagaceae. This flora was dominated by Lauraceae with affinities to Cryptocarya and Litsea, but other families include Araliaceae, Cunoniaceae, Elaeocarpaceae, Euphorbiaceae sensu lato, Menispermaceae, Myrsinaceae, Myrtaceae, Onagraceae, Proteaceae and Sterculiaceae. Many ferns, conifers, and Nothofagus are from lineages with Gondwanan ancestors, whereas other taxa show links to Australia (e.g., Gyrostemonaceae), New Caledonia (e.g., Beauprea) and South America (e.g., Luzuriaga, Fuchsia). Many of these taxa are now extinct in New Zealand, and therefore indicate much wider biogeographic ranges for many families and genera in the past.     

New radiolarian species from the Upper Cretaceous-Lower Paleogene of the eastern slope of the northern Ural Mountains

Five new radiolarian species, Dictyophimus? orbiculiporosus sp. nov., Spongomelissa imperceptusa sp. nov., Theocoronium puncticulatum sp. nov., Pterocyrtidium porrectum sp. nov., and Tripodiscinus corona sp. nov., from the Campanian-Danian diatomites of the Leplinskaya Formation of the northern Ural Mountains are described. They are useful for stratification and correlation of the Upper Cretaceous and Lower Paleogene beds of the Ural Region of Western Siberia.     

Phylogenetic study of clavicipitaceous fungi using acetaldehyde dehydrogenase gene sequences

Aciculosporium and Heteroepichloë (Clavicipitaceae) are characteristic bambusicolous fungi in east Asia. In this study, we examined their intergeneric relationships based on the ALDH1-1 gene, which encodes a member of the aldehyde dehydrogenase family. In the clavicipitaceous fungi examined in this study, the nucleotide sequence of the third exon of ALDH1-1 (Exon-3) is 889 bp in length and has no insertion/deletion. A phylogenetic tree based on Exon-3 indicated that the clavicipitaceous fungi could be divided into two large groups: Cordyceps, Nomuraea, and Ustilaginoidea species formed a paraphyletic group, and the other grass biotrophic species formed a monophyletic group. This monophyletic group was further divided into three groups with high bootstrap support: i.e., species with Neotyphodium anamorphs (e.g., Epichloë), species with Ephelis anamorphs (e.g., Heteroepichloë), and Aciculosporium-Claviceps species. We discuss the relationships among Aciculosporium, Heteroepichloë, and other clavicipitaceous fungi.     

Towards improvement of marker assisted selection of apple scab resistant cultivars: <Emphasis Type="Italic">Venturia inaequalis</Emphasis> virulence surveys and standardization of molecular marker alleles associated with resistance genes

Molecular breeding for pathogen resistance faces two major problems that delay its widespread adoption, resistance breakdown and difficulties in unambiguously identifying the alleles of the markers associated with specific resistance genes. Since the breakdown of the Rvi6 (Vf) gene in the Northern part of Europe breeders have intensified the search for new resistance sources to be introduced into their breeding programs. Alternative major genes to Rvi6 are available (e.g. Rvi2, Rvi4, Rvi5, Rvi10; Rvi11, Rvi12, Rvi13, and Rvi15, respectively Vh2, Vh4, Vm, Va, Vbj, Vb, Vd, Vr2 according to the old apple scab resistance gene nomenclature) but, with few exceptions (i.e., Rvi4, Rvi5 and, Rvi13), they have so far not been incorporated in commercial varieties. Pyramiding, i.e., combining several of these major resistance genes (R-genes) in individual plants, is one of the most promising strategies currently available to develop apple cultivars with durable apple scab resistance. But, which genes are the best suited to produce such new cultivars? Although the most interesting genes are surely those whose resistance so far has not been broken by the pathogen, genes with resistance that has been overcome coupled with only limited spread of the virulence may also be used in the pyramiding process. However, obtaining information on whether an R-gene is overcome and if so, the extent of the spread of the virulence is difficult and time consuming. Furthermore, often such reports are not up-to-date and the correctness of the data is difficult to verify. To solve these problems, the initiative “Monitoring of Venturia inaequalis virulences” has been proposed. The monitoring is based on a network of orchards of selected differential hosts. Incidence and severity of scab on these genotypes will be collected yearly; and after validation, the data will be published through the homepage of the project (www.vinquest.ch). Here, we present an outline of this initiative. A second major obstacle for broad adoption of marker assisted selection is the lack of tools to align marker analyzes performed in different laboratories to unambiguously identify the alleles linked to specific resistances. The identification of the alleles of the markers in coupling with the resistance genes is often very difficult, if the same genotype used to develop the markers is not simultaneously analyzed. In this paper we present an approach to standardize the size of the alleles in coupling with the resistance genes, using easily accessible cultivars. The proposed procedure has been applied to selected markers for the apple scab resistance genes Rvi2, Rvi4, Rvi5, Rvi6, Rvi11, Rvi12, Rvi13, Rvi14 and Rvi15 (respectively Vh2, Vh4, Vm, Vf, Vbj, Vb, Vd, Rvi14 and Vr2 according to the old nomenclature).     

<Emphasis Type="Italic">Athyrium sessilipinnum</Emphasis>: A new lady fern (Athyriaceae) from southern China

A new species of Athyrium from southern China is described and illustrated as Athyrium sessilipinnum. Morphological comparisons among this new species and similar ones (e.g., A. arisanense, A. gedeanum, A. epirachis, and A. otophorum) are provided. Molecular evidence reveals a sister relationship between the new species and A. arisanense. The most distinctive characters of A. sessilipinnum are the sessile, non-pinnatifid and non-shortened pinnae.     

A laboratory study of host use by the cuckoo catfish <Emphasis Type="Italic">Synodontis multipunctatus</Emphasis>

The only known non-avian vertebrate obligate brood parasite is the cuckoo catfish (Synodontis multipunctatus), a Lake Tanganyikan endemic. The cuckoo catfish parasitizes Tanganyikan mouthbrooding cichlids, and under captive conditions, will also parasitize cichlids from other Rift Valley lakes. Here we examine the frequency of parasitism by the cuckoo catfish of Ctenochromis horei from Lake Tanganyika and three species from Lake Malawi and the greater Lake Victorian system in a laboratory setting. C. horei was parasitized significantly less (17%) than the allopatric species Haplochromis latifasciatus, Haplochromis nubilus, and Metriaclima estherae (combined parasitism rate of 28%). The lower rates of parasitism in C. horei may be due to differences in the mating ritual, oviposition (e.g., long periods of pseudo-spawning before actual oviposition), and behavioral adaptations (e.g., increased aggression towards the cuckoo catfish). The number of catfish eggs per parasitized brood was similar between C. horei, H. latifasciatus, H. nubilus, and M. estherae. Our results are comparable to findings from the field for C. horei parasitism frequency and number of cuckoo catfish per brood. We also analyzed the parasitism rate of the albino morph of Metriaclima zebra, a domestic strain. Parasitism rates and number of catfish per brood were the highest in the albino morphotype suggesting that the higher levels of parasitism may be related to lower aggressive behavior, lower visual acuity, or captive influence. Cuckoo catfish and mouthbrooding cichlids provide a model system for testing brood parasitism in a laboratory setting.     

The taxonomic composition,characteristics, and neurotoxic activities of ribbon worm-associated bacteria from the Sea of Japan

The taxonomic composition of bacteria associated with two species of tetrodotoxin-bearing (TTX-bearing) (Hubrechtella juliae and Lineus alborostratus) and two species of non-TTX-bearing (Quasitetrastemma stimpsoni and Malacobdella grossa) ribbon worms collected from the Peter the Great Bay of Sea of Japan was studied. Bacterial isolates were identified using 16S rRNA gene sequencing and phenotypic characteristics. Thirty-eight strains of heterotrophic bacteria from the eight genera: Pseudoalteromonas, Shewanella, Ruegeria, Pseudomonas, Defluviicoccus, Vibrio, Alteromonas, and Bacillus, were isolated and characterized. γ-Proteobacteria dominated among the associated microflora of nemerteans (76.3% of the total number of isolates). Sensitivity analysis of 38 strains to antibiotics of various classes revealed multiple resistance to three or more antibiotics in all of the studied isolates. The 15 bacterial strains isolated in the study exhibited antimicrobial activities against at least one of five indicator microorganisms, most of which corresponded to the Pseudoalteromonas genus. Screening of the TTX-producing bacteria was performed using confocal laserscanning microscopy and polyclonal antibodies. A TTX-producing strain, Pseudoalteromonas sp., was found in the nemertean H. juliae. A correlation between the presence of TTX-positive microflora and the toxicity of nemerteans was determined.     

Salicaceae-Feeding Leaf-Mining Insects in Siberia: Distribution,Trophic Specialization,and Pest Status

This paper provides an overview of the leaf-mining insect community feeding on willows (Salix spp.) and poplars (Populus spp.) in Siberia. According to published data and our own observations, 50 leaf-mining insect species (i.e., 24 species of Lepidoptera, 15 Coleoptera, 6 Diptera, and 5 Hymenoptera) feed on those two plant genera in Siberia. Using an integrative approach combining field work, morphological and DNA barcoding analyses, we identified 32 leaf-mining insect species from 14 regions across Siberia (i.e. 64% of all leaf-mining species known on Salicaceae in this part of Russia). Among them, 26 species most often found in parks and botanical gardens, represented new faunistic records for several poorly explored regions of Siberia. We have more than doubled the list of Salicaceae-feeding leaf-mining insects in Tomsk oblast, Altai krai, and the Republic of Tuva, and for the first time provided data on leaf-miners for the Khanty–Mansi Autonomous Okrug. The micromoth Phyllocnistis gracilistylella (Gracillariidae), recently described from Japan, was found on a new host plant (Salix caprea) in the south of Krasnoyarsk krai, is new for Russia. Eight leafmining insect species (i.e., five gracillariids: Phyllocnistis labyrinthella, Ph. unipunctella, Phyllonorycter apparella, Ph. sagitella, and Ph. populifoliella; two beetles: Zeugophora scutellaris and Isochnus sequensi; and one sawfly: Heterarthrus ochropoda) can outbreak on poplars, most often in urban plantations, botanical gardens, and plant nurseries in Siberia, and can also affect natural stands. Forty-five species of 50 leaf-mining insects known to feed on willow and poplar in Siberia also occur in Central and Eastern Europe. The remaining five species (Phyllocnistis gracilistylella, Phyllonorycter sibirica, Heterarthrus fasciatus, Tachyerges dauricus, and Isochnus arcticus) are recorded in Asia only. Species richness of the family Gracillariidae, the most diverse on Salicaceae in Siberia, displays 80% similarity to that in the European part of Russia and 71% to the Russian Far East. We discuss the faunal similarity of these regions and highlight the importance of applying an integrative approach combining ecological, morphological analyses, and DNA barcoding to explore and characterize the insect fauna of poorly studied regions of Asian part of Russia.     

Glutathione improves survival of cryopreserved embryogenic calli of <Emphasis Type="Italic">Agapanthus praecox</Emphasis> subsp. <Emphasis Type="Italic">orientalis</Emphasis>

The effect of supplementation of reduced glutathione (GSH) to cryoprotectant solution on the generation of reactive oxygen species (ROS) (e.g., H₂O₂, OH^·, and O ₂ ^·? ) and antioxidants (e.g., SOD, POD, CAT, AsA, and GSH), as well as membrane lipid peroxidation (i.e., MDA content) mitigation in cryopreserving of embryogenic calli (EC) of Agapanthus praecox subsp. orientalis was investigated. The vitrification-based cryopreservation method was used in this study. The addition of GSH at a final concentration of 0.08 mM to the cryoprotectant solution has significantly improved cryotolerance of A. praecox EC. The EC post-thaw survival rate increased by 68.34 % using the cryoprotectant solution containing 0.08 mM GSH as compared to the control (GSH-free). EC treated with GSH displayed the reduction in  OH^· generation activity and the contents of H₂O₂ and MDA, as well as enhancement in the inhibition of O ₂ ^·? generation and the antioxidant activity. Treatment with exogenous GSH also increased endogenous AsA and GSH contents after dehydration step. Expression of stress-responsive genes, e.g., peroxidase (POD), peroxiredoxin, ascorbate peroxidase (APX), monodehydroascorbate reductase (MDHAR), and glutathione peroxidase (GPX), was also increased during cryopreservation processes. The expression of DAD1 (Defender against apoptotic cell death) was elevated, while cell death-related protease SBT was suppressed. These results demonstrated that the addition of GSH to cryoprotectant solution affects the ROS level and could effectively improve survival of A. praecox EC through enhancing antioxidant enzyme activities and decreasing cell death.     

Anatomical features of species of Cyperaceae from northeastern Brazil

Seventy-three species from 17 genera of Cyperaceae were studied with the aim of identifying and confirming those species with Kranz anatomy. Among the species studied, 36 exhibited Kranz anatomy; 37 did not. Of the four types of Kranz anatomy recognized in Cyperaceae, three were encountered: the chlorocyperoid type in the genera Cyperus, Kyllinga, Lipocarpha, Pycreus, and Remirea; the fimbristyloid type in Abildgaardia, Bulbostylis, and Fimbristylis; and the rhynchosporoid type in Rhynchospora. Non-Kranz anatomy was confirmed in species of the following genera: Becquerelia, Calyptrocarya, Cyperus, Diplacrum, Eleocharis, Fuirena, Hypolytrum, Pleurostachys, Rhynchospora, and Scleria. The anatomical data obtained corroborate earlier studies of species of Cyperaceae as to the presence of Kranz anatomy and the anatomical types in several species and the “Kranzkette” pattern in Cyperus ligularis and Cyperus pohlli.     

Deciphering signature of selection affecting beef quality traits in Angus cattle

Artificial selection towards a desired phenotype/trait has modified the genomes of livestock dramatically that generated breeds that greatly differ in morphology, production and environmental adaptation traits. Angus cattle are among the famous cattle breeds developed for superior beef quality. This paper aimed at exploring genomic regions under selection in Angus cattle that are associated with meat quality traits and other associated phenotypes. The whole genome of 10 Angus cattle was compared with 11 Hanwoo (A-H) and 9 Jersey (A-J) cattle breeds using a cross-population composite likelihood ratio (XP-CLR) statistical method. The top 1% of the empirical distribution was taken as significant and annotated using UMD3.1. As a result, 255 and 210 genes were revealed under selection from A–H and A–J comparisons, respectively. The WebGestalt gene ontology analysis resulted in sixteen (A–H) and five (A–J) significantly enriched KEGG pathways. Several pathways associated with meat quality traits (insulin signaling, type II diabetes mellitus pathway, focal adhesion pathway, and ECM-receptor interaction), and feeding efficiency (olfactory transduction, tight junction, and metabolic pathways) were enriched. Genes affecting beef quality traits (e.g., FABP3, FTO, DGAT2, ACS, ACAA2, CPE, TNNI1), stature and body size (e.g., PLAG1, LYN, CHCHD7, RPS20), fertility and dystocia (e.g., ESR1, RPS20, PPP2R1A, GHRL, PLAG1), feeding efficiency (e.g., PIK3CD, DNAJC28, DNAJC3, GHRL, PLAG1), coat color (e.g., MC1-R) and genetic disorders (e.g., ITGB6, PLAG1) were found to be under positive selection in Angus cattle. The study identified genes and pathways that are related to meat quality traits and other phenotypes of Angus cattle. The findings in this study, after validation using additional or independent dataset, will provide useful information for the study of Angus cattle in particular and beef cattle in general.     

Molecular identification of tick-borne pathogens in ticks collected from dogs and small ruminants from Greece

Ticks are vectors for a variety of human and animal pathogens (bacteria, protozoa and viruses). In order to investigate the pathogens carried by ticks in Greece, a total of 179 adult ticks (114 female and 65 male) were collected from domestic animals (sheep, goats and dogs) from 14 prefectures of six regions of Greece. Among them, 40 were Dermacentor marginatus, 25 Haemaphysalis parva, 22 H. sulcata, one H. punctata, 13 Ixodes gibbosus, 77 Rhipicephalus sanguineus s.l. and one R. bursa. All ticks were tested for the presence of DNA of Anaplasma spp., Babesia spp., Coxiella burnetii, Rickettsia spp. and Theileria spp. The collected ticks were examined by PCR and reverse line blot (RLB) assay. A prevalence of 20.1% for Anaplasma spp., 15.6% for Babesia spp. (identifying B. bigemina, B. divergens, B. ovis and B. crassa), 17.9% for C. burnetii, 15.1% for Rickettsia spp., and 21.2% for Theileria spp. (identifying T. annulata, T. buffeli/orientalis, T. ovis and T. lestoquardi) was found. The results of this study demonstrate the variety of tick-borne pathogens of animal and human importance circulating in Greece, and that awareness is needed to minimize the risk of infection, especially among farmers and pet owners.     

Resequencing the<Emphasis Type="Italic">Vrs1</Emphasis> gene in Spanish barley landraces revealed reversion of six-rowed to two-rowed spike

Six-rowed spike 1 (Vrs1) is a gene of major importance for barley breeding and germplasm management as it is the main gene determining spike row-type (2-rowed vs. 6-rowed). This is a widely used DUS trait, and has been often associated to phenotypic traits beyond spike type. Comprehensive re-sequencing Vrs1 revealed three two-rowed alleles (Vrs1.b2; Vrs1.b3; Vrs1.t1) and four six-rowed (vrs1.a1; vrs1.a2; vrs1.a3; vrs1.a4) in the natural population. However, the current knowledge about Vrs1 alleles and its distribution among Spanish barley subpopulations is still underexploited. We analyzed the gene in a panel of 215 genotypes, made of Spanish landraces and European cultivars. Among 143 six-rowed accessions, 57 had the vrs1.a1 allele, 83 were vrs1.a2, and three showed the vrs1.a3 allele. Vrs1.b3 was found in most two-rowed accessions, and a new allele was observed in 7 out of 50 two-rowed Spanish landraces. This allele, named Vrs1.b5, contains a ‘T’ insertion in exon 2, originally proposed as the causal mutation giving rise to the six-row vrs1.a2 allele, but has an additional upstream deletion that results in the change of 15 amino acids and a potentially functional protein. We conclude that eight Vrs1 alleles (Vrs1.b2, Vrs1.b3, Vrs1.b5, Vrs1.t1, vrs1.a1, vrs1.a2, vrs1.a3, vrs1.a4) discriminate two and six-rowed barleys. The markers described will be useful for DUS identification, plant breeders, and other crop scientists.     

The structure of the claspettes in the male genitalia of the subgenus <Emphasis Type="Italic">Ochlerotatus</Emphasis> Lynch Arribalzaga of the genus <Emphasis Type="Italic">Aedes</Emphasis> Meigen (Diptera,Culicidae) and their diagnostic significance

The structure of the claspettes (modified projections in the male genitalia) in species of the subgenus Ochlerotatus Lynch Arribalzaga of the genus Aedes Meigen is described in detail. A thorough investigation of the three-dimensional structure of the claspettes is necessary for identification of the Ochlerotatus species from Russia. The study of 30 species of Ochlerotatus demonstrated that frequently the use of the claspette structure as a diagnostic character was incorrect when the claspettes were described as flat structures. Examination of the three-dimensional structure of the claspettes has revealed characters differentiating Aedes diantaeus, A. intrudens and A. pullatus; A. communis, A. punctor, and A. hexodontus; A. annulipes, A. excrucians, and A. euedes, as well as some other species.     

More white verticillium-like anamorphs with erect conidiophores

This study focuses on the former Verticillium section Albo-erecta that included white or whitish species with verticillium-like, erect conidiophores. Its type species was Verticillium fungicola, which was transferred to Lecanicillium, a genus that otherwise contains species with prostrate conidiophores. Phylogenetic analysis of ITS, 18S and 28S rDNA sequences revealed that this group is heterogeneous and its members belong to at least three families. The present study is a first step to its resolution. Supported by analyses of 68 sequences of ITS, 23 sequences of 18S and 43 sequences of 28S ribosomal DNA, the species are distributed over three families. In the Cordycipitaceae, Leptobacillium gen. nov. is described with L. leptobactrum comb. nov. and its new variety, calidius. In the Hypocreaceae, Hypomyces is treated with one new combination from former Nectriopsis, H. tubariicola, and two new anamorphic species, H. ellipsosporus and H. subglobosus; in Sphaerostilbella, one new anamorphic species, S. parabroomeana, is described. In the Bionectriaceae, anamorphic isolates of Nectriopsis requiring a new combination, N. lindauiana, and a new species, N. fuliginicola, are described. Parsimony analysis of the LSU suggests that Ovicillium gen. nov. with four new species, O. attenuatum, O. oosporum, O. subglobosum and O. napiforme, is a member of the Bionectriaceae by 93 % bootstrap support. Of uncertain family classification are Chlamydocillium gen. nov. with one new soil-borne species, C. cyanophilum, and Chlorocillium gen. nov. based on Acremonium griseum Petch. A few further white verticillium-like anamorphs, particularly V. biguttatum, could not yet be reclassified.