A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits.

Rose is the world's most important ornamental plant, with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Roses are outbred and can have various ploidy levels. Our objectives were to develop a high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short reads, and anchoring to a high-density genetic map, and to study the genome structure and genetic basis of major ornamental traits. We produced a doubled haploid rose line ('HapOB') from Rosa chinensis 'Old Blush' and generated a rose genome assembly anchored to seven pseudo-chromosomes (512 Mb with N50 of 3.4 Mb and 564 contigs). The length of 512 Mb represents 90.1-96.1% of the estimated haploid genome size of rose. Of the assembly, 95% is contained in only 196 contigs. The anchoring was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features, including the pericentromeric regions, through annotation of transposable element families and positioned centromeric repeats using fluorescent in situ hybridization. The rose genome displays extensive synteny with the Fragaria vesca genome, and we delineated only two major rearrangements. Genetic diversity was analysed using resequencing data of seven diploid and one tetraploid Rosa species selected from various sections of the genus. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and the number of flower petals. A rose APETALA2/TOE homologue is proposed to be the major regulator of petal number in rose. This reference sequence is an important resource for studying polyploidization, meiosis and developmental processes, as we demonstrated for flower and prickle development. It will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.

Quantitative nanoscale vortex imaging using a cryogenic quantum magnetometer.

Microscopic studies of superconductors and their vortices play a pivotal role in understanding the mechanisms underlying superconductivity. Local measurements of penetration depths or magnetic stray fields enable access to fundamental aspects such as nanoscale variations in superfluid densities or the order parameter symmetry of superconductors. However, experimental tools that offer quantitative, nanoscale magnetometry and operate over large ranges of temperature and magnetic fields are still lacking. Here, we demonstrate the first operation of a cryogenic scanning quantum sensor in the form of a single nitrogen-vacancy electronic spin in diamond, which is capable of overcoming these existing limitations. To demonstrate the power of our approach, we perform quantitative, nanoscale magnetic imaging of Pearl vortices in the cuprate superconductor YBa2Cu3O7-δ. With a sensor-to-sample distance of ∼10 nm, we observe striking deviations from the prevalent monopole approximation in our vortex stray-field images, and find excellent quantitative agreement with Pearl's analytic model. Our experiments provide a non-invasive and unambiguous determination of the system's local penetration depth and are readily extended to higher temperatures and magnetic fields. These results demonstrate the potential of quantitative quantum sensors in benchmarking microscopic models of complex electronic systems and open the door for further exploration of strongly correlated electron physics using scanning nitrogen-vacancy magnetometry.

Strain coupling of a nitrogen-vacancy center spin to a diamond mechanical oscillator.

We report on single electronic spins coupled to the motion of mechanical resonators by a novel mechanism based on crystal strain. Our device consists of single-crystal diamond cantilevers with embedded nitrogen-vacancy center spins. Using optically detected electron spin resonance, we determine the unknown spin-strain coupling constants and demonstrate that our system resides well within the resolved sideband regime. We realize coupling strengths exceeding 10 MHz under mechanical driving and show that our system has the potential to reach strong coupling. Our novel hybrid system forms a resource for future experiments on spin-based cantilever cooling and coherent spin-oscillator coupling.

Human ribosomal protein L7 carries two nucleic acid-binding domains with distinct specificities.

Protein L7 is associated with the large subunit of eukaryotic ribosomes that can act as a co-regulator of nuclear receptor-mediated transcription. In this study we show that L7 carries in addition to the known N-terminal nucleic acid-binding domain (NBD 1) a second one (NBD 2) which maps to the 50 C-terminal amino acids of the protein. The amino acid sequence of this region does not contain any of the known nucleic acid binding motifs; thus, NBD 2 may represent a new class of nucleic acid-binding protein motifs. NBD 2 is conserved in all known eukaryotic L7 homologs, whereas NBD 1 is only present in mammalian L7. Binding studies show that NBD 2 is functionally different from NBD 1 in that it binds preferentially to 28S rRNA, suggesting that NBD 2 is involved in the attachment of protein L7 to the large ribosomal subunit. Potential functions of NBD 1 and NBD 2 in translational and nuclear receptor-mediated transcriptional control are discussed.

Correlation between chlamydial infection and autoimmune response: molecular mimicry between RNA polymerase major sigma subunit from Chlamydia trachomatis and human L7.

L7 is one of the ribosomal proteins frequently targeted by autoantibodies in rheumatic autoimmune diseases. A computer search revealed a region within the immunodominant epitope of L7 (peptide II) that is highly homologous to amino acid sequence 264-286 of the RNA polymerase major sigma factor of the eubacterium Chlamydia trachomatis. Anti-L7 autoantibodies affinity purified from the immunodominant epitope were able to recognize this sequence as they reacted with purified recombinant sigma factor. Immunofluorescence labeling experiments on C. trachomatis lysates revealed a punctate staining pattern of numerous spots when incubated with the affinity-purified anti-peptide II autoantibodies. Binding of autoantibodies to peptide II was inhibited by the homologous sigma peptide. This is the first demonstration of epitope mimicry between a human and a chlamydial protein on the level of B cells. Antibody screening revealed a significant correlation between the presence of anti-L7 autoantibodies and C. trachomatis infection in patients with systemic lupus erythematosus and mixed connective tissue disease. Our results suggest that molecular mimicry is involved in the initiation of anti-L7 autoantibody response and may represent a first glance into the immunopathology of Chlamydia with respect to systemic rheumatic diseases.

Characteristic epitope recognition pattern of autoantibodies against eukaryotic ribosomal protein L7 in systemic autoimmune diseases.

OBJECTIVE: To define the epitope-recognition pattern and the fine specificity of the autoantibody response to protein L7 in patients with rheumatic diseases. METHODS: The epitope-recognition pattern was studied by enzyme-linked immunosorbent assay utilizing overlapping fragments of L7. The fine specificity was examined by binding inhibition and isoelectric focusing. RESULTS: We observed a disease-specific epitope-recognition pattern of anti-L7 autoantibodies. There was one immunodominant epitope that was recognized by all anti-L7-positive sera from patients with systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), and systemic sclerosis (SSc). Additional recognition of minor epitopes was observed; it arises by intramolecular epitope spreading and was correlated with disease activity in SLE patients. SSc patients differed from SLE and RA patients in that their sera did not recognize certain minor epitopes. The major epitope was recognized by high-affinity autoantibodies of limited heterogeneity. Minor epitopes were recognized by heterogeneous low-affinity autoantibodies. CONCLUSION: The anti-L7 autoantibody response is oligoclonal. Additional B cell clones are activated by antigen during active phases of disease.

Autoantibodies against eukaryotic protein L7 in patients suffering from systemic lupus erythematosus and progressive systemic sclerosis: frequency and correlation with clinical, serological and genetic parameters. The SLE Study Group.

Recent studies have shown that sera of patients suffering from systemic autoimmune diseases contain autoantibodies directed against the eukaryotic ribosomal protein L7 [1]. In the present study we screened a large panel of sera from patients with systemic lupus erythematosus (SLE) for the presence of anti-L7 autoantibodies and their relationship to clinical, serological and genetic parameters of SLE. By means of an ELISA employing recombinant protein L7 as antigen we detected anti-L7 autoantobodies in 172 of 506 SLE sera (34%). Negative correlations were observed between the presence of anti-L7 autoantibodies, serum IgG levels and proteinuria; a potentially positive relationship existed with lung fibrosis. In order to analyse further this possibility we screened sera of 129 patients suffering from progressive systemic sclerosis (PSS) for anti-L7 reactivity; 45 of these patients had lung fibrosis. Of the PSS patients, 41% exhibited anti-L7 autoantibodies, but positive reactions were evenly distributed among patients with and without lung fibrosis. Protein L7 thus represents a major autoantigen of systemic autoimmune diseases, but does not so far define a distinct subpopulation of patients.

Influence of X-irradiation on the motor activity of rat urinary bladder in vitro and in vivo.

Preparations of rat detrusor vesicae urinariae exposed to 50 kV X-irradiation with 10 to 200 Gy (single dose) at dose-rates of 30 and 60 Gy/min reacted immediately with a dose and dose-rate dependent reversible or persistent increase (up to ten hours) of the basal tone and an increase or a decrease of the acetylcholine contractile response. The motor activity was recorded isotonically. For measurements of time changes following treatment in vivo the bladder was locally irradiated from lateral position with single 300 kV X-ray doses of 10, 25 and 50 Gy. The motor reaction of isolated detrusor preparations to acetylcholine had a threshold concentration in control animals of 2.3 X 10(-10) mol/l (n = 33); the sensitivity to acetylcholine was diminished as early as one to two hours after local irradiation with 50 Gy as reflected in a ten times higher threshold concentration, which decreased further with time past treatment up to 40 days. The inhibitory effect after 25 Gy was weaker. The contractile response of acetylcholine at different concentrations (10(-10) to 10(-5) mol/l) was also diminished after irradiation (50 Gy). It is suggested that the pathophysiological reactions of the radiogenic bladder are based on multifactorial mechanisms and X-ray induced tonic contraction as well as inhibition of the acetylcholine contractile response could be essential factors for the clinically observed hypertonia of the irradiated bladder ("radiogene Harnblase") and its functional volume decrease as well as of the diminished pressure during micturition.

Reactions of isolated rat aorta to X-irradiation.

The reaction of isolated helical strips of rat aorta to X-irradiation was studied: X-rays (50 kV) induced a reproducible, reversible contractile response at threshold doses of 2.5 Gy (60 Gy/min) and 10 Gy (30 Gy/min). After repeated irradiation with the same doses at equal time intervals and constant dose-rate (for example 50 Gy every 15 min, dose-rate 60 Gy/min) the contractile response was progressively diminished, i.e. a tachyphylaxis appeared. The preparations still reacted even after total doses over 1000 Gy. The X-ray induced contractile responses were dose- and dose-rate dependent. Quantitative analysis indicated no essential differences in the radiation-induced contractile response when recorded under isometric or isotonic conditions. After hypothermia (20 degrees C) or hyperthermia (42 degrees C) no visible radiation response could be induced. Part of the aortic strips were spontaneously active: X-ray doses of 5 to 10 Gy stimulated, while doses of 100 to 200 Gy inhibited or blocked the spontaneous phasic activity. A comparison between the immediate X-ray reaction of vascular and non-vascular smooth muscle preparations is given. Participation of cholinergic and adrenergic mechanisms in the X-ray induced contractions of rat aorta seems to be ruled out, because the blocking agents atropine, phentolamine, and bretylium had no effect.