Establishment of the diploid gynogenetic hybrid clonal line of red crucian carp × common carp

This study investigated the gynogenetic cytobiological behavior of the third gynogenetic generation (G3), which was generated from the diploid eggs produced by the second gynogenetic generation (G2) of red crucian carp × common carp, and determined the chromosomal numbers of G3, G2×scatter scale carp and G2×allotetraploid hybrids of red crucian carp × common carp. The results showed that the diploid eggs of G2 with 100 chromosomes, activated by UV-irradiated sperm from scatter scale carp and without the treatment for doubling the chromosomes, could develop into G3 with 100 chromosomes. Similar to the first and second gynogenetic generations (G1 and G2), G3 was also diploid (2n=100) and presented the hybrid traits. The triploids (3n=150) and tetraploids (4n=200) were produced by crossing G2 with scatter scale carp and crossing G2 with allotetraploids, respectively. The extrusion of the second polar body in the eggs of G2 ruled out the possibility that the retention of the second polar body led to the formation of the diploid eggs. In addition, we discussed the mechanism of the formation of the diploid eggs generated by G2. The establishment of the diploid gynogenesis clonal line (G1, G2 and G3) provided the evidence that the diploid eggs were able to develop into a new diploid hybrid clonal line by gynogenesis. By producing the diploid eggs as a unique reproductive way, the diploid gyno- genetic progeny of allotetraploid hybrids of red crucian carp × common carp had important signifi- cances in both biological evolution and production application.     

Rapd fingerprinting of diploid Lolium perenne × hexaploid Festuca arundinacea hybrid genomes

We tested the application of RAPD technology for identification of hybrid genomes originated from a maternal clone of Lolium perenne L. (2n = 2x = 14) bearing cytoplasmic male sterility, which was pollinated separately by five clones of Festuca arundinacea Schreb. cv. Barocco (2n = 6x = 42). Six classes of RAPD markers were recognized, specific to: 1) Festuca genome and inherited into F1 hybrid genomes, 2) Lolium genome inherited into F1 hybrid genomes, 3) Lolium-specific bands not found in F1 progeny, 4) Festuca-specific bands not found in F1 progeny, 5) new bands found only in F1 hybrid profiles, 6) bands common to all parental and F1 hybrid genotypes. RAPD data were shown to have full potential a) to serve as an unequivocal proof of genome recombination in perennial ryegrass × tall fescue hybrids, b) to identify hybrid genomes, c) to reveal phenetic relationships of the accessions from crossing families, d) to enhance, by fingerprinting, the selection of superior hybrid material for further breeding. RAPD data were found to be consistent with the festucoid phenotype of F1 hybrids. This revised version was published online in July 2006 with corrections to the Cover Date.     

An improved hybrid bream derived from a hybrid lineage of Megalobrama amblycephala (♀)×Culter alburnus (♂)

Science China Life Sciences - Distant hybridization is an important technique in fish genetic breeding. In this study, based on the establishment of an allodiploid fish lineage (BT, 2n=48,...     

Hieracium madoniense (Asteraceae) – a new species from Sicily

Abstract

A new endemic species of Hieracium is described from the Madonie Mountains (northern Sicily). Named Hieracium madoniense, this new taxon is confined to the Rocca di Mele, along the borders of Fagus sylvatica woods, on carbonate substrate. Relationships with the closest taxa are discussed.     

Metallophytes—a view from the rhizosphere

Abundance of Fabaceae declines in representation through post-fire-succession in fynbos vegetation of the Cape Floristic Region (CFR). This reduction in legume occurrence coincides with a known decline in post-fire soil P availability. It was hypothesized that the disappearance of legume species during post-fire succession is due to an inability to acquire P effectively from sparingly soluble sources. P-acquisition strategies and response to P supply were compared between legume (Aspalathus, Cyclopia, Indigofera, Podalyria) and non-legume (Elegia, Leucadendron, Protea) genera when supplied with 1 or 10 mg P kg^?1 dry sand. Each genus consisted of a seeder (non-persistent) and resprouter (persistent) species. Non-legumes showed a greater investment in below-ground biomass, more root clusters, with higher concentrations of carboxylates exuded by cluster roots and carboxylates that were better suited to the mobilization of sparingly soluble P compared to legumes. The growth response to increased P supply was 53% higher in legumes than in non-legumes. The lack of a growth response to an elevated P supply in the non-legumes was attributed to N-limitation. Legume resprouters had a higher investment in cluster-root biomass and a lower capacity to down-regulate P-uptake than the seeders. Therefore the inability to acquire sufficient P from low concentration and sparingly soluble soil P-sources may contribute to the lack of indigenous legume persistence in fynbos vegetation of the CFR.     

Alloantigenic variant selection in vitro from a mouse lymphoma — Sarcoma hybrid

TwoH-2 ^a +/H-2 ^s — alloantigenic loss variants have been obtained from anH-2 ^a +/H-2 ^s + mouse lymphoma/sarcoma hybrid, YACIR/MSWBS, by in vitro selection, with repeated exposure toanti-H-2 ^s serum and complement. Loss of the MSWBS derivedH-2 ^s complex was associated with the loss of the morphologically distinguishable, translocated MSWBS derived chromosomes 17. The morphologically normal YACIR-derived chromosomes 17 were maintained.     

Current knowledge and phytosociological data on the high-altitude vegetation in the Western Carpathians — a review

Presented survey summarizes the results of the studies published predominantly after 2000, dealing with the plant communities around and above the timberline in (montane) subalpine to alpine (subnival) belt of the Western Carpathians. All of these communities underwent a critical syntaxonomical and nomenclatorical revision, hence the demonstrated overview of high-mountain vegetation of Western Carpathians (mostly from Slovakia, less from Poland border areas) represent the current state of knowledge. The high-altitude vegetation database, which is the part of Slovak National Vegetation Database, SNVD (), incorporated 8,160 published relevés on 15 May 2007 (of the total of 30,469 published relevés in the SNVD). Concerning the unpublished relevés, the individual authors have provided more than 18,400 of them to be stored in SNVD; 2,301 of all unpublished relevés could be assigned to high-altitude vegetation. Mountain and alpine vegetation is in SNVD presented by 15 classes; the most frequent class is Mulgedio-Aconitetea. With its quantity and also the quality of relevés, the high-altitude database, as well as the whole SNVD, represents the unique database within Slovakia, which provides information not only about the locality, floristic composition and variability of individual vegetation types, but also about several environmental variables such as inclination, aspect, geology or soil type, characteristic for individual relevés. Together with other Central European databases, SNVD takes up the leading position in Europe.     

Gene mapping of 28S and 5S rDNA sites in the spined loach Cobitis taenia (Pisces, Cobitidae) from a diploid population and a diploid–tetraploid population

We compare the chromosomal 28S and 5S rDNA patterns of the spined loach C. taenia (2n = 48) from an exclusively diploid population and from a diploid–polyploid population using 28S and 5S rDNA probe preparation and labelling, and fluorescence in situ hybridization (FISH). The 5S rDNA was located in two to three chromosome pairs, and separated from the 28S loci for the males and one female (F1) from the diploid population. Loaches from a diploid–polyploid population, and one female (F2) from the diploid population were characterized by at least one chromosome pair with 5S and 28S overlapping signals. The fishes differed mainly in their number of 28S rDNA loci, located on 3–6 chromosomes. All individuals from both populations were characterized by one acrocentric chromosome bearing a 28S rDNA signal on the telomeres of its long arm. The number of major ribosomal DNA in the karyotype of C. taenia by FISH was always higher than the number of Ag-NORs. Our data confirm the extensive polymorphism of NORs in both populations, as already has been observed in closely related Cobitis species, and less polymorphic 5S rDNA pattern. However, this preliminary result highlights the need for a wider scale study.     

Assessing structural variation in a personal genome—towards a human reference diploid genome

Background

Characterizing large genomic variants is essential to expanding the research and clinical applications of genome sequencing. While multiple data types and methods are available to detect these structural variants (SVs), they remain less characterized than smaller variants because of SV diversity, complexity, and size. These challenges are exacerbated by the experimental and computational demands of SV analysis. Here, we characterize the SV content of a personal genome with Parliament, a publicly available consensus SV-calling infrastructure that merges multiple data types and SV detection methods.

Results

We demonstrate Parliament’s efficacy via integrated analyses of data from whole-genome array comparative genomic hybridization, short-read next-generation sequencing, long-read (Pacific BioSciences RSII), long-insert (Illumina Nextera), and whole-genome architecture (BioNano Irys) data from the personal genome of a single subject (HS1011). From this genome, Parliament identified 31,007 genomic loci between 100 bp and 1 Mbp that are inconsistent with the hg19 reference assembly. Of these loci, 9,777 are supported as putative SVs by hybrid local assembly, long-read PacBio data, or multi-source heuristics. These SVs span 59 Mbp of the reference genome (1.8%) and include 3,801 events identified only with long-read data. The HS1011 data and complete Parliament infrastructure, including a BAM-to-SV workflow, are available on the cloud-based service DNAnexus.

Conclusions

HS1011 SV analysis reveals the limits and advantages of multiple sequencing technologies, specifically the impact of long-read SV discovery. With the full Parliament infrastructure, the HS1011 data constitute a public resource for novel SV discovery, software calibration, and personal genome structural variation analysis.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1479-3) contains supplementary material, which is available to authorized users.     

Characterization of a new human diploid cell line—IMR-91

Summary A human diploid fibroblast cell line has been established from the lung tissue of a male fetus. This has been characterized and frozen away in large quantity. A smaller quantity of fibroblastlike cells from skin has also been established, partially characterized, and placed in frozen storage from the same fetus. This project is in support of the National Institute on Aging research in general cell biology. The present lines designated IMR-91 lung and IMR-91 skin complement the previous human diploid fibroblast culture (IMR-90) established from a female fetus. The lack of random inactivation of one of the two X chromosomes in the present male line reduces the genetic heterogeneity inherent in the female line.     

An intergeneric hybrid,Campostoma anomalum × Rhinichthys atratulus,from the Youghiogheny River drainage,West Virginia

The first record of a natural intergeneric hybrid of Campostoma anomalum × Rhinichthys atratulus is described from the Youghiogheny River drainage. Morphometric and meristic characters of the parents and hybrid were used to calculate a mean hybrid index value of 49.8. Dentition of the hybrid was intermediate as was intestinal coiling. In addition to the hybrid index, C. anomalum, R. atratulus and the hybrid were examined electrophoretically. Of the 32 enzymatic loci resolved, six (ADH-A, EST-B, LDH-A, PGM-A, SDH-B and SOD-C) showed hybrid inheritance patterns identical to the enzyme pattern obtained by mixing tissue extracts composed of the two parental species.     

Preliminary experiments on resource competition between a migrating and a non-migrating clone of the hybrid D. galeata×hyalina

Competition experiments between two clones of thehybrid D. galeata × hyalina differing invertical migration behaviour were carried out in thelaboratory, in a set-up which separated the clonesspatially. The influence of fish kairomones,artificial predation and the imitation of dielvertical migration circumstances were investigated. Inthe presence of fish kairomones, the non-migratingclone outnumbered the migrating one. The introductionof artificial predation reduced this effect in such away that the migrating clone had a competitiveadvantage over the non-migrating clone. It wasconcluded that competition results do not contradictlife history studies performed with the same twoclones, since the presence of fish kairomones enhancesthe reproduction of the non-migrating clone more thanthat of the migrating one.     

Electrophoretic confirmation of the intergeneric hybrid ×Ruttyruspolia (Acanthaceae)

A plant collected in South Africa in the early 1960's has been considered an intergeneric hybrid with the parental taxa beingRuspolia hypocrateriformis (Vahl)Milne-Redhead var.australis Milne-Redhead andRuttya ovata Harv. The intermediate morphology of the plant provided the strongest evidence of its hybrid origin. The natural hybrid, named formally as ×Ruttyruspolia A. Meeuse & de Wet, is highly sterile. Crosses between the two presumed parental taxa produced two plants that are very similar to the putative natural hybrid. We had examined the presumed parental species and the natural and artificial hybrids using enzyme electrophoresis. The two parental species are highly differentiated at genes specifying soluble enzymes; they have a genetic identity of 0.51. They have no common alleles at two genes, and contain alternative alleles in very different frequencies at two loci.Ruttya andRuspolia exhibit both unique and common alleles at two additional genes. The natural and artificially produced plants of ×Ruttyruspolia are identical electrophoretically and contain alleles unique to each of the parental species at two genes. In addition, individuals of ×Ruttyruspolia combine alternative high frequency alleles from each parent at two loci. Allozymes provide strong confirming evidence for the hybrid origin of naturally occurring ×Ruttyruspolia because the products of specific alleles either unique to or highly characteristic of the two putative parental taxa are found combined in ×Ruttyruspolia.     

Characterization of α-gliadin genes from diploid wheats and the comparative analysis with those from polyploid wheats

To carry out comparative analysis of the α-gliadin genes on A genomes of diploid and polyploid wheats, 8 full-length α-gliadin genes, including 3 functional genes and 5 pseudogenes, were obtained from diploid wheats, among which 2, 2 and 4 α-gliadin genes were isolated from T. urartu, T. monococcum, and T. boeoticum, respectively. The results indicated that higher number of α-gliadin pseudogenes have been present in diploid wheats before the formation of polyploid wheats. Amino acid sequence comparative analysis among 26 α-gliadin genes, including 16 functional genes and 10 pseudogenes, from diploid and polyploid wheats was conducted. The results indicated that all α-gliadins contained four coeliac toxic peptide sequences (i.e., PSQQ, QQQP, QQPY, and QPYP). The polyglutamine domains are highly variable, and the second polyglutamine stretch is usually disrupted by the lysine or arginine residue at the fourth position. The unique domain I is the most conserved domain. There are four and two conserved cysteine residues in the unique domains I and II, respectively. Comparative analysis indicated that the functional α-gliadin genes from A genome are highly conserved, whereas the identity of pseudogenes in diploid wheats are higher than those in hexaploid wheats. Phylogenetic analysis indicated that all the analyzed functional α-gliadin genes could be clustered into two major groups, among which one group could be further divided into 5 subgroups. The origin of α-gliadin pseudogene and functional genes were also discussed. The text was submitted by the authors in English.     

Grid user requirements—2004: a perspective from the trenches

Pervasive Grid adoption is predicated on the availability of widely deployed usable software and a user community willing to use it. Currently, widespread adoption of Grids, even within technically sophisticated communities, is limited, and determining and eliminating these barriers to adoption are essential in order for Grids to becoming widely capitalized. Through a series of face-to-face interviews conducted during the summer of 2004, we have identified issues relating to job submission, file transfer, usability, and systems management that must be resolved in order to improve the usability of Grid infrastructures. The background to these issues and some possible solutions are described in this paper.

A diverse deep‐marine Ichnofauna from the Eocene Tarcau sandstone of the Eastern Carpathians,Romania

The Paleocene to Middle Eocene Tarcau Sandstone at Buzau Valley, eastern Carpathians, Romania, records sedimentation in a turbidite system. These strata contain a diverse and abundant pre‐ and postdepositional ichnofauna consisting of 35 ichnogenera and 54 ichnospecies. The predepositional assemblage is rich in graphoglyptids and ornate grazing trails; simple grazing trails, resting traces, and feeding structures also occur. The predepositional assemblage includes Acan‐thorhaphe, Belorhaphe, Cardioichnus, Circulichnus, Coch‐lichnus, Cosmorhaphe, Desmograpton, Fustiglyphus, Gordia, Helicolithus, Helminthopsis, Helminthorhaphe, Lorenzinia, Megagrapton, Paleodictyon, Paleomeandron, Protopaleodictyon, Scolicia (S. strozzii), Spirorhaphe, Spirophycus, Treptichnus, and Urohelminthoida. The ich‐nodiversity, composition, ethology, and morphologic complexity of the predepositional association are indicative of the Nereites ichnofacies. The postdepositional association essentially consists of dwelling, feeding, and grazing traces, and is represented by Chondrites, Glockerichnus, Halopoa, Nereites, Ophiomorpha, Phycodes, Planolites, Polykampton, Scolicia(S. prisca. S. striata), Taenidium, Thalassinoides, and Zoophycos. Palaeophycus occurs in both assemblages. Allochthonous Teredolites is present in wood fragments, The postdepositional association includes elements of the Skolithos ichnofacies and facies‐crossing forms that are commonly present in deep‐marine deposits, Elements of the Skolithos ichnofacies are present not only in the most proximal parts of the turbidite system, but also in distal parts. The number of predepositional forms greatly exceeds postdepositional ones, reflecting a dominance of K‐selected over r‐selected population strategies in a stable environment. High levels of ichnodiversity in the Tarcau Sandstone are comparable with deep‐sea ichnofaunas from the Polish Carpathians and with other flysch trace‐fossil assemblages of similar age. This abundant and diverse Eocene ichnofauna supports the idea of extremely rich deep‐sea ichnofaunas in the Cenozoic.     

Plant regeneration from interspecific hybrid and backcross progeny of Helianthus eggertii × Helianthus annuus

An efficient protocol for plant regeneration from leaves of the interspecific hybrid Helianthus eggertii Small. × Helianthus annuus L. was developed. The regeneration capacity of the first backcross progeny is reported. Leaves from the F1 interspecific hybrid were cultured on Murashige and Skoog basal media (MS) supplemented with -naphthalenacetic acid (NAA), N ⁶-benzyladenine (BA), AgNO₃, KNO₃, casein hydrolysate and adenine sulfate. Embryo-like structures and/or shoots regeneration were observed on most of the tested media. The best results were obtained on media with a higher concentration of cytokinin (8.8 M BA) and lower concentration of auxin (1.08 M NAA). The addition of casein hydrolysate in the media increased the regeneration efficiency. Plant regeneration was achieved via somatic embryogenesis and direct organogenesis. The regeneration potential of leaf, stem and root explants of eighteen first backcross lines was studied. Most of the tested lines were highly regenerable and some of them had DNA content closely related to that of Helianthus annuus L.     

Vegetation history in the Eastern Romanian Carpathians: pollen analysis of two sequences from the Mohoş crater

Two sequences of about 10.5 m originating from a peat bog in Romania were analysed for pollen (202 and 127 pollen spectra). The vegetation history, supported by 24 ¹⁴C dates is described since the Late Glacial. At the onset of the Holocene Ulmus first appears, together with Betula. Among the main components of the Quercetum mixtum (Quercus, Fraxinus, Tilia, Corylus) that became established almost simultaneously by around 9000 B.P., Quercus frequencies rarely exceed 10%. The local establishment of Carpinus is about 6000 b.p. Its maximum occurred between 4500 and 3000 b.p. Fagus pollen is regularly recorded since 8000 b.p. Its absolute dominance tooks place at about 3000 b.p. Picea pollen is present since the Late Glacial. The first indications of human activities appear at around 6500 b.p.     

Mechanisms of dominance by the invasive hybrid cattail Typha?×?glauca

The mechanisms by which invasive plants displace native species are often not well elucidated, limiting knowledge of invasion dynamics and the scientific basis for management responses. Typha × glauca Godr. invades wetlands throughout much of North America. Like other problematic wetland invaders, Typha is large, grows densely, and leaves behind copious litter. It thus has the potential to impact wetlands both in life and after death. We assessed patterns in field settings and used simulated wetland-plant communities to experimentally test abiotic and community responses to live Typha, Typha litter, and water-level differences (confounded in the field) using a full-factorial design. In general, litter was a stronger driver of change than live Typha. The greatest impacts were seen where, as in nature, live and dead Typha co-occurred. Live-Typha treatments did not differ from controls in light or temperature conditions but did reduce community biomass and alter community composition. Litter strongly affected light, temperature and its variability, community and species-level plant biomass, and community composition. Interactions between live Typha and litter affected aspects of plant-community composition. Advantageously for Typha, interspecific litter effects were not mirrored by intraspecific suppression of live Typha. These findings clarify how Typha is such an effective invader. Similar mechanisms are likely involved in invasions by other plant species, particularly in wetlands. Managers should respond quickly to new Typha invasions and, when dealing with established stands, remove litter in addition to eradicating live plants.