Measurement of the

^{140}Ce(n,γ) is a key reaction for slow neutron-capture (s-process) nucleosynthesis due to being a bottleneck in the reaction flow. For this reason, it was measured with high accuracy (uncertainty ≈5%) at the n_TOF facility, with an unprecedented combination of a high purity sample and low neutron-sensitivity detectors. The measured Maxwellian averaged cross section is up to 40% higher than previously accepted values. Stellar model calculations indicate a reduction around 20% of the s-process contribution to the Galactic cerium abundance and smaller sizeable differences for most of the heavier elements. No variations are found in the nucleosynthesis from massive stars.

A strange case of Transthyretin Cardiac Amyloidosis in the Elderly: a diagnostic challenge.

Abstract: Transthyretin (TTR)-related cardiac amyloidosis is a progressive infiltrative cardiomyopathy that mimics hypertensive, hypertrophic heart disease and may go undiagnosed. We here report the case of a 83-year-old woman, which has rapresented an unique case of transthyretin-related cardiac amyloidosis, as a patient with an initial diagnosis of hypertensive heart disease later develops an infiltrative cardiomyopathy due to amyloid deposits.

High genomic variability in the plant pathogenic bacterium Pectobacterium parmentieri deciphered from de novo assembled complete genomes.

BACKGROUND: Pectobacterium parmentieri is a newly established species within the plant pathogenic family Pectobacteriaceae. Bacteria belonging to this species are causative agents of diseases in economically important crops (e.g. potato) in a wide range of different environmental conditions, encountered in Europe, North America, Africa, and New Zealand. Severe disease symptoms result from the activity of P. parmentieri virulence factors, such as plant cell wall degrading enzymes. Interestingly, we observe significant phenotypic differences among P. parmentieri isolates regarding virulence factors production and the abilities to macerate plants. To establish the possible genomic basis of these differences, we sequenced 12 genomes of P. parmentieri strains (10 isolated in Poland, 2 in Belgium) with the combined use of Illumina and PacBio approaches. De novo genome assembly was performed with the use of SPAdes software, while annotation was conducted by NCBI Prokaryotic Genome Annotation Pipeline. RESULTS: The pan-genome study was performed on 15 genomes (12 de novo assembled and three reference strains: P. parmentieri CFBP 8475T, P. parmentieri SCC3193, P. parmentieri WPP163). The pan-genome includes 3706 core genes, a high number of accessory (1468) genes, and numerous unique (1847) genes. We identified the presence of well-known genes encoding virulence factors in the core genome fraction, but some of them were located in the dispensable genome. A significant fraction of horizontally transferred genes, virulence-related gene duplications, as well as different CRISPR arrays were found, which can explain the observed phenotypic differences. Finally, we found also, for the first time, the presence of a plasmid in one of the tested P. parmentieri strains isolated in Poland. CONCLUSIONS: We can hypothesize that a large number of the genes in the dispensable genome and significant genomic variation among P. parmentieri strains could be the basis of the potential wide host range and widespread diffusion of P. parmentieri. The obtained data on the structure and gene content of P. parmentieri strains enabled us to speculate on the importance of high genomic plasticity for P. parmentieri adaptation to different environments.

Elevated serum uric acid concentration at discharge confers additive prognostic value in elderly patients with acute heart failure.

BACKGROUND AND AIMS: Elevated serum uric acid (sUA) concentrations have been associated with worse prognosis in heart failure (HF) but little is known about elderly patients. We aimed to assess long-term additive prognostic value of sUA in elderly patients hospitalized for HF. METHODS AND RESULTS: Clinical and echocardiographic characteristics of 310 consecutive elderly patients hospitalized for HF were collected. During index period, 206 had sUA concentrations available, which were obtained within 24 h prior to discharge; 10 patients were lost to follow-up, leaving 196 patients available. Patients had a median age of 77 (IQR 69-83) years, and were mostly male (64.5%). sUA ranges for tertiles I-III were: 1.5-6.1, 6.2-8.3, and 8.4-18.9 mg/dl, respectively. During a median follow-up of 27 months (IQR 10.5-39.5), 122 combined events occurred (87 deaths and 73 HF rehospitalizations). Four-year event-free survival for the combined endpoint was 46 ± 7% for tertile I, 34 ± 7% for tertile II, and 21 ± 5% for tertile III (P = 0.001). By multivariable Cox backward analysis, sUA was retained as a significant predictor. Compared with the lowest sUA tertile, tertile III showed a strong association with outcome, also after adjustment for other predictors (HR 1.84, 95% CI 1.16-2.93; P = 0.01). Importantly, addition of sUA to the other significant predictors of outcome resulted in improved risk classification (net reclassification improvement 0.19, P = 0.017). CONCLUSIONS: High sUA at discharge is a strong predictor of adverse outcome in elderly hospitalized for HF, and it significantly improves risk classification. Measuring sUA can be a simple and useful tool to identify high-risk elderly hospitalized for HF.

Draft Genome Sequence of a Highly Virulent Strain of the Plant Pathogen Dickeya solani, IFB0099.

Dickeya solani is an important bacterial pathogen of potato cultivars in Europe. Here, we present the draft genome of D. solani strain IFB0099 isolated from potato in Poland that shows a high level of pectinolytic activity and a high virulence. This genome sequence is 5,094,121 bp and contains 4,365 protein-coding sequences.

Novel method to study neutron capture of 235U and 238U simultaneously at keV energies.

The neutron capture cross sections of the main uranium isotopes, (235)U and (238)U, were measured simultaneously for keV energies, for the first time by combining activation technique and atom counting of the reaction products using accelerator mass spectrometry. New data, with a precision of 3%-5%, were obtained from mg-sized natural uranium samples for neutron energies with an equivalent Maxwell-Boltzmann distribution of kT ∼ 25 keV and for a broad energy distribution peaking at 426 keV. The cross-section ratio of (235)U(n,γ)/(238)U(n,γ) can be deduced in accelerator mass spectrometry directly from the atom ratio of the reaction products (236)U/(239)U, independent of any fluence normalization. Our results confirm the values at the lower band of existing data. They serve as important anchor points to resolve present discrepancies in nuclear data libraries as well as for the normalization of cross-section data used in the nuclear astrophysics community for s-process studies.

StreamingTrim 1.0: a Java software for dynamic trimming of 16S rRNA sequence data from metagenetic studies.

Next-generation sequencing technologies are extensively used in the field of molecular microbial ecology to describe taxonomic composition and to infer functionality of microbial communities. In particular, the so-called barcode or metagenetic applications that are based on PCR amplicon library sequencing are very popular at present. One of the problems, related to the utilization of the data of these libraries, is the analysis of reads quality and removal (trimming) of low-quality segments, while retaining sufficient information for subsequent analyses (e.g. taxonomic assignment). Here, we present StreamingTrim, a DNA reads trimming software, written in Java, with which researchers are able to analyse the quality of DNA sequences in fastq files and to search for low-quality zones in a very conservative way. This software has been developed with the aim to provide a tool capable of trimming amplicon library data, retaining as much as taxonomic information as possible. This software is equipped with a graphical user interface for a user-friendly usage. Moreover, from a computational point of view, StreamingTrim reads and analyses sequences one by one from an input fastq file, without keeping anything in memory, permitting to run the computation on a normal desktop PC or even a laptop. Trimmed sequences are saved in an output file, and a statistics summary is displayed that contains the mean and standard deviation of the length and quality of the whole sequence file. Compiled software, a manual and example data sets are available under the BSD-2-Clause License at the GitHub repository at https://github.com/GiBacci/StreamingTrim/.

[ITS-polymorphism of salt-tolerant and salt-sensitive native isolates of Sinorhizoblum meliloti--symbionts of alfalfa, clover and fenugreek plants].

Polymorphism of rrs-rrl sequence of ribosomal operons (intergenic sequence, ITS) was studied among 81 isolates of Sinorhizobium meliloti (AK001-AK210) derived from the collection of alfalfa nodulating bacteria of the Laboratory of genetics of ARRIAM, by using species-specific primers FGPS 1490/FGPL132VM. Isolates were obtained from nodules of different species of wild host plants from Medicago, Melilotus and Trigonella genera grown in salinized North-Western region of Kazakhstan. The typical structure of ITS, similar to that of test strain Rm1021, was dominant in native rhizobia population, while in one third of the isolates (33.3%) this sequence was divergent. Among the latter, the ITS type of strain AK83 (RCAM00182) was dominant. Here, we show for the first time that isolates with reduced level of salt-tolerance had more diverse intergenic sequences of rrn-operons. No phylogenetic separation was observed between isolates grouped on the basis of their tolerance or sensitivity towards 0.6 M NaCl. However, the frequency of divergent ITS types within the two groups of rhizobia depended on the host symbiotic preference observed in natural environment, allowing to speculate about the existence of a chromosome types specific for S. meliloti isolates with differential salt tolerance. In conclusion, we propose that in the area subjected to secondary salinization, which are also the centre of introgressive hybridization of alfalfa, micro-evolutionary processes, affecting rrn-operons and associated with salt adaptation, are also occurring in symbiotic root nodule bacteria populations.

Comparison of periodontal microbiological patterns in Italian spouses.

PURPOSE: The aim of this study is to evaluate whether periodontopathogens are transmitted from husband to wife or vice versa. MATERIALS AND METHODS: We tested the microbiological profile of 9 couples married for at least 10 years suffering from periodontitis. The microbiological analysis provides the quantification by Real-Time PCR of six main periodontopathogens, including P. gingivalis, T. denticola, T. forsythia, F. nucleatum ssp. polymorphum, P. intermedia, A. actinomycetemcomitans and genotype of P. gingivalis FimA in 90 subgingival plaque samples. RESULTS: The microbiological profiles highlighted a quite similar composition of oral microbial flora among husband and wife. Statistical results revealed a very high Pearson correlation values for the microbiological profiles in all 9 spouses. Additionally, five couples out of nine showed statistically similar values for the microbiological profile as determined by the Wilcoxon rank Sign test. We provided also a strong validation for the horizontal transmission of oral pathogens in the detection of the same genotype of P. gingivalis FimA in the spouses. CONCLUSIONS: The presence of periodontitis in one member of the couple is a strong indicator of risk for the colonization of the spouse by periodontophatic bacteria. This study confirms that periodontal disease can be transmitted suggesting the importance of an early detection of oral pathogens in familial pattern of periodontitis to clarify the source of infection in order to assess correct prevention protocols based on potential infectivity within spouses.

Contrasting patterns of genetic divergence in two sympatric pseudo-metallophytes: Rumex acetosa L. and Commelina communis L.

BACKGROUND: Patterns of genetic divergence between populations of facultative metallophytes have been investigated extensively. However, most previous investigations have focused on a single plant species making it unclear if genetic divergence shows common patterns or, conversely, is species-specific. The herbs Rumex acetosa L. and Commelina communis L. are two pseudo-metallophytes thriving in both normal and cupriferous soils along the middle and lower reaches of the Yangtze River in China. Their non-metallicolous and metallicolous populations are often sympatric thus providing an ideal opportunity for comparative estimation of genetic structures and divergence under the selective pressure derived from copper toxicity. RESULTS: In the present study, patterns of genetic divergence of R. acetosa and C. communis , including metal tolerance, genetic structure and genetic relationships between populations, were investigated and compared using hydroponic experiments, AFLP, ISSR and chloroplast genetic markers. Our results show a significant reduction in genetic diversity in metallicolous populations of C. communis but not in R. acetosa . Moreover, genetic differentiation is less in R. acetosa than in C. communis , the latter species also shows a clustering of its metallicolous populations. CONCLUSIONS: We propose that the genetic divergences apparent in R. acetosa and C. communis , and the contrasting responses of the two species to copper contamination, might be attributed to the differences in their intrinsic physiological and ecological properties. No simple and generalised conclusions on genetic divergence in pseudo-metallophytes can thus be drawn.

VDR TaqI polymorphism is associated with chronic periodontitis in Italian population.

AIM: The aim of this study is to investigate the relationship between a vitamin D receptor polymorphism and the diagnosis of periodontal disease in non-smoker Italian patients with aggressive and chronic periodontitis. MATERIALS AND METHODS: DNA was obtained from the internal cheek mucosa of 115 patients with chronic periodontitis, 58 with aggressive periodontitis and 65 healthy controls. Allelic discrimination was performed using TaqMan SNP Genotyping Assays. Genotype and allele frequencies were calculated. RESULTS: Comparisons between diseased patients and healthy controls showed significant differences. Moreover, calculating the odds ratio, individuals with the TT genotype, was more susceptible than individuals with tt to chronic periodontitis and individuals with Tt to aggressive periodontitis. Interestingly, the dominant model (TT + Tt vs. tt) was applicable to chronic periodontitis, whilst for aggressive periodontitis the recessive model (TT vs. Tt + tt) gave the highest odds ratio. CONCLUSIONS: These data indicated that VDR TaqI polymorphism is differentially associated with development of chronic periodontitis and aggressive periodontitis in Italian population. The study of VDR polymorphisms may therefore be essential for the prevention of periodontitis and for a pre-treatment periodontal and/or for implant assessment. Moreover VDR TaqI polymorphism could be useful to discriminate between aggressive and chronic forms of periodontal disease.

Relationship between heavy metals pollution and genetic diversity in Mediterranean populations of the sandhopper Talitrus saltator (Montagu) (Crustacea, Amphipoda).

Trace metals are one of the groups of pollutants that reduce genetic variability in natural populations, causing the phenomenon known as "genetic erosion". In this study we evaluate the relationship between trace metals contamination (Hg, Cd and Cu) and genetic variability, assessed using fluorescent Inter-Simple Sequence Repeats (fISSRs). We used eight populations of a well-established biomonitor of trace metals on sandy beaches: the amphipod Talitrus saltator. The trace metals analysis confirmed the ability of sandhoppers to accumulate Hg, Cd and Cu. Moreover, populations from sites with high Hg availability had the lowest values of genetic diversity. Our results validate the use of fISSR markers in genetic studies in sandhoppers and support the "genetic erosion" hypothesis by showing the negative influence of Hg contamination on sandhopper genetic diversity. Therefore, genetic variability assessed with fISSR markers could be successfully employed as a biomarker of Hg exposure.

Development of real-time PCR assay for detection and quantification of Sinorhizobium meliloti in soil and plant tissue.

AIMS: Sinorhizobium meliloti is a nitrogen-fixing alpha-proteobacterium present in soil and symbiotically associated with root nodules of leguminous plants. To date, estimation of bacterial titres in soil is achieved by most-probable-number assays based on the number of nodules on the roots of test plants. Here, we report the development of two real-time PCR (qPCR) assays to detect the presence of S. meliloti in soil and plant tissues by targeting, in a species-specific fashion, the chromosomal gene rpoE1 and the pSymA gene nodC. METHODS AND RESULTS: rpoE1 and nodC primer pairs were tested on DNA extracted from soil samples unspiked and spiked with known titres of S. meliloti and from plant root samples nodulated with S. meliloti. Results obtained were well in agreement with viable titres of S. meliloti cells estimated in the same samples. CONCLUSIONS: The developed qPCR assays appear to be enough sensitive, precise and species-specific to be used as a complementary tool for S. meliloti titre estimation. SIGNIFICANCE AND IMPACT OF THE STUDY: These two novel markers offer the possibility of quick and reliable estimation of S. meliloti titres in soil and plant roots contributing new tools to explore S. meliloti biology and ecology including viable but nonculturable fraction.

Halo structure of the island of inversion nucleus 31Ne.

The cross sections for single-neutron removal from the very neutron-rich nucleus 31Ne on Pb and C targets have been measured at 230 MeV/nucleon using the RIBF facility at RIKEN. The deduced large Coulomb breakup cross section of 540(70) mb is indicative of a soft E1 excitation. Comparison with direct-breakup model calculations suggests that the valence neutron of 31Ne occupies a low-l orbital (most probably 2p(3/2)) with a small separation energy (S(n) approximately < 0.8 MeV), instead of being predominantly in the 1f(7/2) orbital as expected from the conventional shell ordering. These findings suggest that 31Ne is the heaviest halo system known.

Genetic diversity of bacterial communities of serpentine soil and of rhizosphere of the nickel-hyperaccumulator plant Alyssum bertolonii.

Serpentine soils are characterized by high levels of heavy metals (Ni, Co, Cr), and low levels of important plant nutrients (P, Ca, N). Because of these inhospitable edaphic conditions, serpentine soils are typically home to a very specialized flora including endemic species as the nickel hyperaccumulator Alyssum bertolonii. Although much is known about the serpentine flora, few researches have investigated the bacterial communities of serpentine areas. In the present study bacterial communities were sampled at various distances from A. bertolonii roots in three different serpentine areas and their genetic diversity was assessed by terminal restriction fragment length polymorphism (T-RFLP) analysis. The obtained results indicated the occurrence of a high genetic diversity and heterogeneity of the bacterial communities present in the different serpentine areas. Moreover, TRFs (terminal restriction fragments) common to all the investigated A. bertolonii rhizosphere samples were found. A new cloning strategy was applied to 27 TRFs that were sequenced and taxonomically interpreted as mainly belonging to Gram-positive and alpha-Proteobacteria representatives. In particular, cloned TRFs which discriminated between rhizosphere and soil samples were mainly interpreted as belonging to Proteobacteria representatives.

Enrichment and identification of bacteria capable of reducing chemical oxygen demand of anaerobically treated molasses spent wash.

AIMS: The aim of this study was to isolate and identify bacterial strains capable of using recalcitrant compounds of molasses spent wash as sole carbon source from the soils of abandoned sites of distillery effluent discharge and characterize their ability of reducing the chemical oxygen demand (COD) of the spent wash. METHODS AND RESULTS: The isolates were grouped into six haplotypes by amplified ribosomal DNA restriction analysis (ARDRA) and BOX-PCR. The phylogenetic position of the representatives of the six main haplotypes strains was determined by 16S rDNA sequencing. They showed maximum similarity to six genera viz. Pseudomonas, Enterobacter, Stenotrophomonas, Aeromonas, Acinetobacter and Klebsiella. The extent of COD (44%) reduced collectively by the six strains was equal to that reduced individually by Aeromonas, Acinetobacter, Pseudomonas and Enterobacter. With spent wash as sole carbon source, the COD reducing strains grew faster at 37 degrees C than 30 degrees C. CONCLUSIONS: Bacterial strains capable of degrading some of the recalcitrant compounds of anaerobically digested molasses spent wash can be isolated from the soils of abandoned sites of distillery effluent discharge. Biostimulation of these bacteria, which can degrade 44% of the carbon compounds of anaerobically digested molasses spent wash can be achieved by nitrogen fertilization and relatively higher temperature. SIGNIFICANCE AND IMPACT OF THE STUDY: Supplementation of nitrogen source and controlling the temperature can be used in evolving strategies for in situ bioremediation of anaerobically digested spent wash from distilleries.

Evolutionary dynamics of nickel hyperaccumulation in Alyssum revealed by its nrDNA analysis.

• Molecular phylogeny based on ribosomal internal transcribed spacer (ITS) sequences was studied to investigate the phyletic relationships among some nickel (Ni)-hyperaccumulating and nonhyperaccumulating species of the genus Alyssum in relation to their geographic distribution and Ni-hyperaccumulating phenotype. • Thirty-seven samples belonging to 32 taxa were analysed by sequencing the polymerase chain reaction-amplified ITS region and performing neighbor joining, maximum parsimony and maximum likelihood phylogenetic analyses. • The ITS region in the sampled species varied from 221 to 307 bp of ITS1 and from 194 to 251 bp of ITS2. A total of 765 characters was used to infer the phylogeny and the average nucleotide variation detected was 15.15%. • Nickel-hyperaccumulation could have been lost or acquired independently more than once during the speciation of the genus. The geographical location of species could not be related to phylogenetic affinities.

Chloroplast genetic diversity and biogeography in the serpentine endemic Ni-hyperaccumulator Alyssum bertolonii.

• Chloroplast microsatellites (cpSSR) were used to analyze the patterns of genetic variation within and among populations of the serpentine endemic, Alyssum bertolonii . • Thirty-five different chloroplast haplotypes were identified in 90 plants sampled from nine populations originating from the four disjunct northern-Italian serpentine regions where the species is found. • High levels of genetic diversity were found within each of the populations sampled. Analysis of Molecular Variance (AMOVA) showed high degrees of differentiation among both different populations of the same serpentine region and different regions (Φ ST = 0.622, Φ CT = 0.252, respectively). • The results indicated that: each population was established by few founders and then subsequently differentiated the existing chloroplast haplotypes; each population is a distinct genetic entity; and populations within the same serpentine region are more related than populations from different regions.