Tracking the implementation of NCCLS M100-S12 expanded-spectrum cephalosporin MIC breakpoints for nonmeningeal isolates of Streptococcus pneumoniae by clinical laboratories in the United States during 2002 and 2003

BACKGROUND: The Performance Standards for Antimicrobial Susceptibility Testing, Twelfth Informational Supplement, M100-S12, published by the National Committee for Clinical Laboratory Standards (NCCLS) in January 2002 introduced distinct minimum inhibitory concentration (MIC) interpretative breakpoints for ceftriaxone, cefotaxime, and cefepime for nonmeningeal isolates of Streptococcus pneumoniae. Previously, a single set of interpretative breakpoints was used for both meningeal and nonmeningeal isolates. METHODS: To estimate the rate of adoption of the M100-S12 interpretive breakpoints by clinical laboratories, antimicrobial susceptibility test results for ceftriaxone and cefotaxime from nonmeningeal S. pneumoniae isolates were studied using data collected from January 2002 to June 2003 by The Surveillance Network(® )Database – USA (TSN(®)), an electronic surveillance database. RESULTS: Of the 262 laboratories that provided data that could be evaluated, 67.6% had adopted the M100-S12 breakpoints one and one-half years after they were published. CONCLUSIONS: The NCCLS M100-S12 recommendation to interpret MICs to expanded-spectrum cephalosporins using two distinct sets of breakpoints for meningeal and nonmeningeal isolates of S. pneumoniae was steadily implemented by clinical microbiology laboratories in the United States following their initial publication in January 2002. The use of these new breakpoints more accurately reflects the clinical activities of expanded-spectrum cephalosporins than did the single set of interpretative breakpoints previously used for both meningeal and nonmeningeal isolates

New γ\gamma-ray Transitions Observed in 19^{19}Ne with Implications for the 15^{15}O(α\alpha,γ\gamma)19^{19}Ne Reaction Rate

The $^{15}$O($\alpha$,$\gamma$)$^{19}$Ne reaction is responsible for breakout from the hot CNO cycle in Type I x-ray bursts. Understanding the properties of resonances between $E_x = 4$ and 5 MeV in $^{19}$Ne is crucial in the calculation of this reaction rate. The spins and parities of these states are well known, with the exception of the 4.14- and 4.20-MeV states, which have adopted spin-parities of 9/2$^-$ and 7/2$^-$, respectively. Gamma-ray transitions from these states were studied using triton-$\gamma$-$\gamma$ coincidences from the $^{19}$F($^{3}$He,$t\gamma$)$^{19}$Ne reaction measured with GODDESS (Gammasphere ORRUBA Dual Detectors for Experimental Structure Studies) at Argonne National Laboratory. The observed transitions from the 4.14- and 4.20-MeV states provide strong evidence that the $J^\pi$ values are actually 7/2$^-$ and 9/2$^-$, respectively. These assignments are consistent with the values in the $^{19}$F mirror nucleus and in contrast to previously accepted assignments

Key 19^{19}Ne states identified affecting γ\gamma-ray emission from 18^{18}F in novae

Detection of nuclear-decay $\gamma$ rays provides a sensitive thermometer of nova nucleosynthesis. The most intense $\gamma$-ray flux is thought to be annihilation radiation from the $\beta^+$ decay of $^{18}$F, which is destroyed prior to decay by the $^{18}$F($p$,$\alpha$)$^{15}$O reaction. Estimates of $^{18}$F production had been uncertain, however, because key near-threshold levels in the compound nucleus, $^{19}$Ne, had yet to be identified. This Letter reports the first measurement of the $^{19}$F($^{3}$He,$t\gamma$)$^{19}$Ne reaction, in which the placement of two long-sought 3/2$^+$ levels is suggested via triton-$\gamma$-$\gamma$ coincidences. The precise determination of their resonance energies reduces the upper limit of the rate by a factor of $1.5-17$ at nova temperatures and reduces the average uncertainty on the nova detection probability by a factor of 2.1.Comment: 6 pages, 4 figure

Evolution and Association Analysis of Ghd7 in Rice

Plant height, heading date, and yield are the main targets for rice genetic improvement. Ghd7 is a pleiotropic gene that controls the aforementioned traits simultaneously. In this study, a rice germplasm collection of 104 accessions (Oryza sativa) and 3 wild rice varieties (O.rufipogon) was used to analyze the evolution and association of Ghd7 with plant height, heading date, and yield. Among the 104 accessions, 76 single nucleotide polymorphisms (SNPs) and six insertions and deletions were found within a 3932-bp DNA fragment of Ghd7. A higher pairwise π and θ in the promoter indicated a highly diversified promoter of Ghd7. Sixteen haplotypes and 8 types of Ghd7 protein were detected. SNP changes between haplotypes indicated that Ghd7 evolved from two distinct ancestral gene pools, and independent domestication processes were detected in indica and japonica varietals respectively. In addition to the previously reported premature stop mutation in the first exon of Ghd7, which caused phenotypic changes of multiple traits, we found another functional C/T mutation (SNP S_555) by structure-based association analysis. SNP S_555 is located in the promoter and was related to plant height probably by altering gene expression. Moreover, another seven SNP mutations in complete linkage were found to be associated with the number of spikelets per panicle, regardless of the photoperiod. These associations provide the potential for flexibility of Ghd7 application in rice breeding programs

New γ -ray transitions observed in Ne 19 with implications for the O 15 (α,γ) Ne 19 reaction rate

The O15(α,γ)Ne19 reaction is responsible for breakout from the hot CNO cycle in type I x-ray bursts. Understanding the properties of resonances between Ex=4 and 5 MeV in Ne19 is crucial in the calculation of this reaction rate. The spins and parities of these states are well known, with the exception of the 4.14- and 4.20-MeV states, which have adopted spin-parities of 9/2- and 7/2-, respectively. γ-ray transitions from these states were studied using triton-γ-γ coincidences from the F19(He3,tγ)Ne19 reaction measured with the GODDESS (Gammasphere ORRUBA Dual Detectors for Experimental Structure Studies) at Argonne National Laboratory. The observed transitions from the 4.14- and 4.20-MeV states provide strong evidence that the Jπ values are actually 7/2- and 9/2-, respectively. These assignments are consistent with the values in the F19 mirror nucleus and in contrast to previously accepted assignments

γ -ray spectroscopy of astrophysically important states in Ca 39

Background: Nova explosions synthesize elements up to A≃40, and discrepancies exist between calculated and observed abundances of Ar and Ca created in the explosion. The K38(p,γ)Ca39 reaction rate has been shown to be influential on these isotopic abundances at the endpoint of nova nucleosynthesis. The energies of the three most important resonances, corresponding to Jπ=5/2+ excited states in the Ca39 nucleus above the proton separation threshold, are uncertain and one has been measured with conflicting values [Er=679(2) versus Er=701(2) keV] in previous experiments. Purpose: Reducing the uncertainties on the resonance energies would allow for a better understanding of the reaction rate. To improve these uncertainties, we searched for γ rays from the depopulation of the corresponding excited states in Ca39. Methods: We report a new measurement of these resonance energies via the observation of previously unobserved γ-ray transitions. These transitions were observed by studying the Ca40(3He,αγ)Ca39 reaction with Gammasphere ORRUBA Dual Detectors for Experimental Structure Studies (GODDESS). The updated resonance energies were then used to calculate the K38(p,γ)Ca39 reaction rate and assess its uncertainties. Results: In total, 23 new transitions were found, including three γ-ray transitions corresponding to the three Jπ=5/2+ states of astrophysical interest at energies of 6156.2(16), 6268.8(22), and 6470.8(19) keV. These correspond to resonance energies in the K38(p,γ)Ca39 reaction of 386(2), 498(2), and 701(2) keV. Conclusions: Updated K38(p,γ)Ca39 reaction rate calculations show a reduced upper limit at nova temperatures. However, the lower-than-previously-measured energy of the 498-keV resonance and uncertainty in its resonance strength increases the upper limit of the rate close to previous estimates at 0.4 GK

A sequence-based genetic linkage map as a reference for Brassica rapa pseudochromosome assembly

<p>Abstract</p> <p>Background</p> <p><it>Brassica rapa </it>is an economically important crop and a model plant for studies concerning polyploidization and the evolution of extreme morphology. The multinational <it>B. rapa </it>Genome Sequencing Project (BrGSP) was launched in 2003. In 2008, next generation sequencing technology was used to sequence the <it>B. rapa </it>genome. Several maps concerning <it>B. rapa </it>pseudochromosome assembly have been published but their coverage of the genome is incomplete, anchoring approximately 73.6% of the scaffolds on to chromosomes. Therefore, a new genetic map to aid pseudochromosome assembly is required.</p> <p>Results</p> <p>This study concerns the construction of a reference genetic linkage map for <it>Brassica rapa</it>, forming the backbone for anchoring sequence scaffolds of the <it>B. rapa </it>genome resulting from recent sequencing efforts. One hundred and nineteen doubled haploid (DH) lines derived from microspore cultures of an F1 cross between a Chinese cabbage (<it>B. rapa </it>ssp. <it>pekinensis</it>) DH line (Z16) and a rapid cycling inbred line (L144) were used to construct the linkage map. PCR-based insertion/deletion (InDel) markers were developed by re-sequencing the two parental lines. The map comprises a total of 507 markers including 415 InDels and 92 SSRs. Alignment and orientation using SSR markers in common with existing <it>B. rapa </it>linkage maps allowed ten linkage groups to be identified, designated A01-A10. The total length of the linkage map was 1234.2 cM, with an average distance of 2.43 cM between adjacent marker loci. The lengths of linkage groups ranged from 71.5 cM to 188.5 cM for A08 and A09, respectively. Using the developed linkage map, 152 scaffolds were anchored on to the chromosomes, encompassing more than 82.9% of the <it>B. rapa </it>genome. Taken together with the previously available linkage maps, 183 scaffolds were anchored on to the chromosomes and the total coverage of the genome was 88.9%.</p> <p>Conclusions</p> <p>The development of this linkage map is vital for the integration of genome sequences and genetic information, and provides a useful resource for the international <it>Brassica </it>research community.</p

Transposable Elements Are a Major Cause of Somatic Polymorphism in Vitis vinifera L.

Through multiple vegetative propagation cycles, clones accumulate mutations in somatic cells that are at the origin of clonal phenotypic diversity in grape. Clonal diversity provided clones such as Cabernet-Sauvignon N°470, Chardonnay N° 548 and Pinot noir N° 777 which all produce wines of superior quality. The economic impact of clonal selection is therefore very high: since approx. 95% of the grapevines produced in French nurseries originate from the French clonal selection. In this study we provide the first broad description of polymorphism in different clones of a single grapevine cultivar, Pinot noir, in the context of vegetative propagation. Genome sequencing was performed using 454 GS-FLX methodology without a priori, in order to identify and quantify for the first time molecular polymorphisms responsible for clonal variability in grapevine. New generation sequencing (NGS) was used to compare a large portion of the genome of three Pinot noir clones selected for their phenotypic differences. Reads obtained with NGS and the sequence of Pinot noir ENTAV-INRA® 115 sequenced by Velasco et al., were aligned on the PN40024 reference sequence. We then searched for molecular polymorphism between clones. Three types of polymorphism (SNPs, Indels, mobile elements) were found but insertion polymorphism generated by mobile elements of many families displayed the highest mutational event with respect to clonal variation. Mobile elements inducing insertion polymorphism in the genome of Pinot noir were identified and classified and a list is presented in this study as potential markers for the study of clonal variation. Among these, the dynamic of four mobile elements with a high polymorphism level were analyzed and insertion polymorphism was confirmed in all the Pinot clones registered in France