Latest results on b-hadron spectroscopy from CDF

B-hadron spectroscopy presents an interesting window for the study of QCD. CDF has performed a number of studies involving the production and spectroscopy of B mesons. Among these studies are the first direct observation of the Bc, and the first observation of both narrow states of the Bs**. In addition, measurements are made of the B** masses and widths and the best limit on the production of Eta_b is set.Comment: Proceedings of the EPS talk given on HEP 2007 in Mancheste

Below Average Midsummer to Early Autumn Precipitation Evolved Into the Main Driver of Sudden Scots Pine Vitality Decline in the Swiss Rhône Valley

The vitality of Scots pine (Pinus sylvestris L.) is declining since the 1990s in many European regions. This was mostly attributed to the occurrence of hotter droughts, other climatic changes and secondary biotic stressors. However, it is still not well understood which specific atmospheric trends and extremes caused the observed spatio-temporal dieback patterns. In the Swiss Rhône valley, we identified negative precipitation anomalies between midsummer and early autumn as the main driver of sudden vitality decline and dieback events. Whereas climate change from 1981 to 2018 did not lead to a reduced water input within this time of the year, the potential evapotranspiration strongly increased in spring and summer. This prolonged and intensified the period of low soil moisture between midsummer and autumn, making Scots pines critically dependent on substantial precipitation events which temporarily reduce the increased water stress. Thus, local climate characteristics (namely midsummer to early autumn precipitation minima) are decisive for the spatial occurrence of vitality decline events, as the lowest minima outline the most affected regions within the Swiss Rhône valley. Mortality events will most likely spread to larger areas and accelerate the decline of Scots pines at lower elevations, whereas higher altitudes may remain suitable Scots pine habitats. The results from our regional study are relevant on larger geographic scales because the same processes seem to play a key role in other European regions increasingly affected by Scots pine dieback events

Drought effects on carbon allocation to resin defences and on resin dynamics in old-grown Scots pine

Droughts and other rapid changes in abiotic environmental conditions can predispose trees to damage by pest insects and pathogens. For survival of coniferous trees, functional resin-based defences are essential, and it is important to know how they react to changes in environmental conditions at various time scales. We studied the effects of differing water availabilities on resin-based defences in mature Scots pine (Pinus sylvestris) trees in a naturally drought-prone forest within a long-term irrigation experiment. Our objectives were to understand the effects of long-term drought on carbon allocation to resin production and to analyse its influence on resin flow and pressure in comparison to the shorter-term effects of seasonal drought. We tracked carbon allocation to resin after C-13-pulse labelling experiment in late summer 2017 and compared the observed resin dynamics between drought-exposed control trees and irrigated trees from June to August during the dry hot summer of 2018. Dry control trees showed higher allocation of labelled carbon to resin than irrigated trees. Resin pressure was higher in dry control than in irrigated trees with similar water potentials, and resin flow in June was higher in dry control than in irrigated trees with similar crown transparency. Yet, resin pressures of dry control trees in particular decreased with decreasing water availability from June to August. Resin flow was little affected by short-term changes in water availability and mostly associated with crown transparency. We suggest that because of differing timescales of direct drought effects and changes in allocation patterns, dry conditions may support resin-based defences in the long term, but a drought period decreases resin pressure in the short term.Peer reviewe

A candidate gene for fire blight resistance in Malus × robusta 5 is coding for a CC-NBS-LRR

Fire blight is the most important bacterial disease in apple (Malus ×  domestica) and pear (Pyrus communis) production. Today, the causal bacterium Erwinia amylovora is present in many apple- and pear-growing areas. We investigated the natural resistance of the wild apple Malus ×  robusta 5 against E. amylovora, previously mapped to linkage group 3. With a fine-mapping approach on a population of 2,133 individuals followed by phenotyping of the recombinants from the region of interest, we developed flanking markers useful for marker-assisted selection. Open reading frames were predicted on the sequence of a BAC spanning the resistance locus. One open reading frame coded for a protein belonging to the NBS-LRR family. The in silico investigation of the structure of the candidate resistance gene against fire blight of M. ×  robusta 5, FB_MR5, led us hypothesize the presence of a coiled-coil region followed by an NBS and an LRR-like structure with the consensus ‘LxxLx[IL]xxCxxLxxL'. The function of FB_MR5 was predicted in agreement with the decoy/guard model, that FB_MR5 monitors the transcribed RIN4_MR5, a homolog of RIN4 of Arabidopsis thaliana that could interact with the previously described effector AvrRpt2EA of E. amylovor

Drought effects on volatile organic compound emissions from Scots pine stems

Tree stems have been identified as sources of volatile organic compounds (VOCs) that play important roles in tree defence and atmospheric chemistry. Yet, we lack understanding on the magnitude and environmental drivers of stem VOC emissions in various forest ecosystems. Due to the increasing importance of extreme drought, we studied drought effects on the VOC emissions from mature Scots pine (Pinus sylvestris L.) stems. We measured monoterpenes, acetone, acetaldehyde and methanol emissions with custom-made stem chambers, online PTR-MS and adsorbent sampling in a drought-prone forest over the hot-dry summer of 2018 and compared the emission rates and dynamics between trees in naturally dry conditions and under long-term irrigation (drought release). The pine stems were significant monoterpene sources. The stem monoterpene emissions potentially originated from resin, based on their similar monoterpene spectra. The emission dynamics of all VOCs followed temperature at a daily scale, but monoterpene and acetaldehyde emission rates decreased nonlinearly with drought over the summer. Despite the dry conditions, large peaks of monoterpene, acetaldehyde and acetone emissions occurred in late summer potentially due to abiotic or biotic stressors. Our results highlight the potential importance of stem emissions in the ecosystem VOC budget, encouraging further studies in diverse environments.Peer reviewe

A candidate gene for fire blight resistance in Malus × robusta 5 is coding for a CC-NBS-LRR

Erworben im Rahmen der Schweizer Nationallizenzen (http://www.nationallizenzen.ch)Fire blight is the most important bacterial disease in apple (Malus ×  domestica) and pear (Pyrus communis) production. Today, the causal bacterium Erwinia amylovora is present in many apple- and pear-growing areas. We investigated the natural resistance of the wild apple Malus ×  robusta 5 against E. amylovora, previously mapped to linkage group 3. With a fine-mapping approach on a population of 2,133 individuals followed by phenotyping of the recombinants from the region of interest, we developed flanking markers useful for marker-assisted selection. Open reading frames were predicted on the sequence of a BAC spanning the resistance locus. One open reading frame coded for a protein belonging to the NBS–LRR family. The in silico investigation of the structure of the candidate resistance gene against fire blight of M. ×  robusta 5, FB_MR5, led us hypothesize the presence of a coiled-coil region followed by an NBS and an LRR-like structure with the consensus ‘LxxLx[IL]xxCxxLxxL’. The function of FB_MR5 was predicted in agreement with the decoy/guard model, that FB_MR5 monitors the transcribed RIN4_MR5, a homolog of RIN4 of Arabidopsis thaliana that could interact with the previously described effector AvrRpt2EA of E. amylovora

Growth and resilience responses of Scots pine to extreme droughts across Europe depend on predrought growth conditions

Global climate change is expected to further raise the frequency and severity of extreme events, such as droughts. The effects of extreme droughts on trees are difficult to disentangle given the inherent complexity of drought events (frequency, severity, duration, and timing during the growing season). Besides, drought effects might be modulated by trees’ phenotypic variability, which is, in turn, affected by long-term local selective pressures and management legacies. Here we investigated the magnitude and the temporal changes of tree-level resilience (i.e., resistance, recovery, and resilience) to extreme droughts. Moreover, we assessed the tree-, site-, and drought-related factors and their interactions driving the tree-level resilience to extreme droughts. We used a tree-ring network of the widely distributed Scots pine (Pinus sylvestris) along a 2,800 km latitudinal gradient from southern Spain to northern Germany. We found that the resilience to extreme drought decreased in mid-elevation and low productivity sites from 1980–1999 to 2000–2011 likely due to more frequent and severe droughts in the later period. Our study showed that the impact of drought on tree-level resilience was not dependent on its latitudinal location, but rather on the type of sites trees were growing at and on their growth performances (i.e., magnitude and variability of growth) during the predrought period. We found significant interactive effects between drought duration and tree growth prior to drought, suggesting that Scots pine trees with higher magnitude and variability of growth in the long term are more vulnerable to long and severe droughts. Moreover, our results indicate that Scots pine trees that experienced more frequent droughts over the long-term were less resistant to extreme droughts. We, therefore, conclude that the physiological resilience to extreme droughts might be constrained by their growth prior to drought, and that more frequent and longer drought periods may overstrain their potential for acclimation.Fondo Europeo de Desarrollo Regional (FEDER) IJCI-2015-25845, UPO-1263216, UHU-1266324Ministerio de Ciencia, Innovación y Universidades RTI2018- 096884-B-C31, RTI2018-096884-B-C33German Waldklimafond FKZ 28WC-4-077-01Bavarian State Ministry for Food, Agriculture, and Forestry ST32

Pentaplexed quantitative real-time PCR assay for the simultaneous detection and quantification of botulinum neurotoxin-producing clostridia in food and clinical samples

Botulinum neurotoxins are produced by the anaerobic bacterium Clostridium botulinum and are divided into seven distinct serotypes (A to G) known to cause botulism in animals and humans. In this study, a multiplexed quantitative real-time PCR assay for the simultaneous detection of the human pathogenic C. botulinum serotypes A, B, E, and F was developed. Based on the TaqMan chemistry, we used five individual primer-probe sets within one PCR, combining both minor groove binder- and locked nucleic acid-containing probes. Each hydrolysis probe was individually labeled with distinguishable fluorochromes, thus enabling discrimination between the serotypes A, B, E, and F. To avoid false-negative results, we designed an internal amplification control, which was simultaneously amplified with the four target genes, thus yielding a pentaplexed PCR approach with 95% detection probabilities between 7 and 287 genome equivalents per PCR. In addition, we developed six individual singleplex real-time PCR assays based on the TaqMan chemistry for the detection of the C. botulinum serotypes A, B, C, D, E, and F. Upon analysis of 42 C. botulinum and 57 non-C. botulinum strains, the singleplex and multiplex PCR assays showed an excellent specificity. Using spiked food samples we were able to detect between 10(3) and 10(5) CFU/ml, respectively. Furthermore, we were able to detect C. botulinum in samples from several cases of botulism in Germany. Overall, the pentaplexed assay showed high sensitivity and specificity and allowed for the simultaneous screening and differentiation of specimens for C. botulinum A, B, E, and F

Combining miRNA and mRNA Expression Profiles in Wilms Tumor Subtypes

Wilms tumor (WT) is the most common childhood renal cancer. Recent findings of mutations in microRNA (miRNA) processing proteins suggest a pivotal role of miRNAs in WT genesis. We performed miRNA expression profiling of 36 WTs of different subtypes and four normal kidney tissues using microarrays. Additionally, we determined the gene expression profile of 28 of these tumors to identify potentially correlated target genes and affected pathways. We identified 85 miRNAs and 2107 messenger RNAs (mRNA) differentially expressed in blastemal WT, and 266 miRNAs and 1267 mRNAs differentially expressed in regressive subtype. The hierarchical clustering of the samples, using either the miRNA or mRNA profile, showed the clear separation of WT from normal kidney samples, but the miRNA pattern yielded better separation of WT subtypes. A correlation analysis of the deregulated miRNA and mRNAs identified 13,026 miRNA/mRNA pairs with inversely correlated expression, of which 2844 are potential interactions of miRNA and their predicted mRNA targets. We found significant upregulation of miRNAs-183, -301a/b and -335 for the blastemal subtype, and miRNAs-181b, -223 and -630 for the regressive subtype. We found marked deregulation of miRNAs regulating epithelial to mesenchymal transition, especially in the blastemal subtype, and miRNAs influencing chemosensitivity, especially in regressive subtypes. Further research is needed to assess the influence of preoperative chemotherapy and tumor infiltrating lymphocytes on the miRNA and mRNA patterns in WT