Microevolution of Helicobacter pylori during prolonged infection of single hosts and within families

Our understanding of basic evolutionary processes in bacteria is still very limited. For example, multiple recent dating estimates are based on a universal inter-species molecular clock rate, but that rate was calibrated using estimates of geological dates that are no longer accepted. We therefore estimated the short-term rates of mutation and recombination in Helicobacter pylori by sequencing an average of 39,300 bp in 78 gene fragments from 97 isolates. These isolates included 34 pairs of sequential samples, which were sampled at intervals of 0.25 to 10.2 years. They also included single isolates from 29 individuals (average age: 45 years) from 10 families. The accumulation of sequence diversity increased with time of separation in a clock-like manner in the sequential isolates. We used Approximate Bayesian Computation to estimate the rates of mutation, recombination, mean length of recombination tracts, and average diversity in those tracts. The estimates indicate that the short-term mutation rate is 1.4×10−6 (serial isolates) to 4.5×10−6 (family isolates) per nucleotide per year and that three times as many substitutions are introduced by recombination as by mutation. The long-term mutation rate over millennia is 5–17-fold lower, partly due to the removal of non-synonymous mutations due to purifying selection. Comparisons with the recent literature show that short-term mutation rates vary dramatically in different bacterial species and can span a range of several orders of magnitude

Efeitos da estimulação da sucção não nutritiva com dedo enluvado na transição alimentar em recém-nascido prematuro de muito baixo peso

Objetivos analisar os efeitos da estimulação da sucção não nutritiva com a técnica do dedo enluvado, sobre o início e a transição alimentar da via gástrica para a via oral em prematuros de muito baixo peso. Métodos estudo aleatório, prospectivo, longitudinal, experimental e controlado, que incluiu 40 prematuros internados na UTI Neonatal do Hospital de Clínicas, com idade gestacional £ 32 semanas e peso de nascimento £ 1500g, clinicamente estáveis. Os prematuros foram distribuídos aleatoriamente, por meio de sorteio, em 2 grupos: grupo controle, sem SNN e grupo experimental, com SNN com dedo enluvado, 3 vezes ao dia, 3 dias na semana. Foram avaliados critérios quanto ao escore da avaliação da prontidão para início da alimentação oral, intercorrências durante a sucção nutritiva (SN) e o tempo de transição alimentar. Resultados quando comparado o grupo experimental em relação ao grupo controle observou-se um escore significantemente maior na avaliação da prontidão para início da alimentação via oral, uma menor frequência de sinais de estresse durante a sucção nutritiva e um menor tempo de transição alimentar da via gástrica para via oral. Conclusão a estimulação da sucção não nutritiva com a técnica do dedo enluvado melhorou a prontidão do prematuro para início da alimentação via oral, diminuiu a frequência dos sinais de estresse durante a alimentação via oral e reduziu o tempo de transição alimentar no grupo experimental quando comparado ao grupo controle

Inhibition of CCN6 (WISP3) expression promotes neoplastic progression and enhances the effects of insulin-like growth factor-1 on breast epithelial cells

INTRODUCTION: CCN6/WISP3 belongs to the CCN (Cyr61, CTGF, Nov) family of genes that contains a conserved insulin-like growth factor (IGF) binding protein motif. CCN6 is a secreted protein lost in 80% of the aggressive inflammatory breast cancers, and can decrease mammary tumor growth in vitro and in vivo. We hypothesized that inhibition of CCN6 might result in the loss of a growth regulatory function that protects mammary epithelial cells from the tumorigenic effects of growth factors, particularly IGF-1. METHOD: We treated human mammary epithelial (HME) cells with a CCN6 hairpin short interfering RNA. RESULTS: CCN6-deficient cells showed increased motility and invasiveness, and developed features of epithelial-mesenchymal transition (EMT). Inhibition of CCN6 expression promoted anchorage-independent growth of HME cells and rendered them more responsive to the growth effects of IGF-1, which was coupled with the increased phosphorylation of IGF-1 receptor and insulin receptor substrate-1 (IRS-1). CONCLUSION: Specific stable inhibition of CCN6 expression in HME cells induces EMT, promotes anchorage-independent growth, motility and invasiveness, and sensitizes mammary epithelial cells to the growth effects of IGF-1

Health information technology implementation - impacts and policy considerations: a comparison between Israel and Portugal

The use of Information and Communications Technology (ICT) in health systems is increasing worldwide. While it is assumed that ICT holds great potential to make health services more efficient and grant patients more empowerment, research on these trends is at an early stage. Building on a study of the impact of ICT on physicians and patients in Israel, a Short Term Scientific Mission (STSM) sponsored by COST Net in conjunction with CIES/ISCTE IUL (Portugal) facilitated a comparison of ICT in health in Israel and Portugal. The comparison focused on patient empowerment, physician behavior and the role of government in implementing ICT. The research in both countries was qualitative in nature. In-depth interviews with the Ministry of Health (MOH), the private sector, patients associations, health plans and researchers were used to collect data. Purposeful sampling was used to select respondents, and secondary sources were used for triangulation. The findings indicate that respondents in both countries feel that patient empowerment has indeed been furthered by introduction of ICT. Regarding physicians, in both countries ICT is seen as providing more information that can be used in medical decision making. Increased access of patients to web-based medical information can strengthen the role of patients in decision making and improve the physician-patient relationship, but also shift the latter in ways that may require adjustments in physician orientation. Physician uptake of ICT in both countries involves overcoming certain barriers, such as resistance to change. At the national level, important differences were found between the two countries. While in Israel, ICT was promoted and adopted by the meso level of the health system, in particular the health plans and government intervention can be found in a later stage, in Portugal the government was the main developer and national strategies were built from the beginning. These two approaches present different advantages and disadvantages. Government involvement in earlier stages could provide benefit in terms of interoperability of systems between different healthcare organizations. However, innovation could be slowed down due to government bureaucracy or lack of leadership. The work provides information in order to understand and improve ICT services. Additionally, it provides input regarding impact of ICT on the physician/patient relationship and national policies in the area

Translational Selection Is Ubiquitous in Prokaryotes

Codon usage bias in prokaryotic genomes is largely a consequence of background substitution patterns in DNA, but highly expressed genes may show a preference towards codons that enable more efficient and/or accurate translation. We introduce a novel approach based on supervised machine learning that detects effects of translational selection on genes, while controlling for local variation in nucleotide substitution patterns represented as sequence composition of intergenic DNA. A cornerstone of our method is a Random Forest classifier that outperformed previous distance measure-based approaches, such as the codon adaptation index, in the task of discerning the (highly expressed) ribosomal protein genes by their codon frequencies. Unlike previous reports, we show evidence that translational selection in prokaryotes is practically universal: in 460 of 461 examined microbial genomes, we find that a subset of genes shows a higher codon usage similarity to the ribosomal proteins than would be expected from the local sequence composition. These genes constitute a substantial part of the genome—between 5% and 33%, depending on genome size—while also exhibiting higher experimentally measured mRNA abundances and tending toward codons that match tRNA anticodons by canonical base pairing. Certain gene functional categories are generally enriched with, or depleted of codon-optimized genes, the trends of enrichment/depletion being conserved between Archaea and Bacteria. Prominent exceptions from these trends might indicate genes with alternative physiological roles; we speculate on specific examples related to detoxication of oxygen radicals and ammonia and to possible misannotations of asparaginyl–tRNA synthetases. Since the presence of codon optimizations on genes is a valid proxy for expression levels in fully sequenced genomes, we provide an example of an “adaptome” by highlighting gene functions with expression levels elevated specifically in thermophilic Bacteria and Archaea

Measurement of the inclusive and dijet cross-sections of b-jets in pp collisions at sqrt(s) = 7 TeV with the ATLAS detector

The inclusive and dijet production cross-sections have been measured for jets containing b-hadrons (b-jets) in proton-proton collisions at a centre-of-mass energy of sqrt(s) = 7 TeV, using the ATLAS detector at the LHC. The measurements use data corresponding to an integrated luminosity of 34 pb^-1. The b-jets are identified using either a lifetime-based method, where secondary decay vertices of b-hadrons in jets are reconstructed using information from the tracking detectors, or a muon-based method where the presence of a muon is used to identify semileptonic decays of b-hadrons inside jets. The inclusive b-jet cross-section is measured as a function of transverse momentum in the range 20 < pT < 400 GeV and rapidity in the range |y| < 2.1. The bbbar-dijet cross-section is measured as a function of the dijet invariant mass in the range 110 < m_jj < 760 GeV, the azimuthal angle difference between the two jets and the angular variable chi in two dijet mass regions. The results are compared with next-to-leading-order QCD predictions. Good agreement is observed between the measured cross-sections and the predictions obtained using POWHEG + Pythia. MC@NLO + Herwig shows good agreement with the measured bbbar-dijet cross-section. However, it does not reproduce the measured inclusive cross-section well, particularly for central b-jets with large transverse momenta.Comment: 10 pages plus author list (21 pages total), 8 figures, 1 table, final version published in European Physical Journal