Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori

Background Horizontal gene transfer is central to evolution in most bacterial species. The detection of exchanged regions is often based upon analysis of compositional characteristics and their comparison to the organism as a whole. In this study we describe a new methodology combining aspects of established signature analysis with textual analysis approaches. This approach has been used to analyze the two available genome sequences of H. pylori. Results This gene-by-gene analysis reveals a wide range of genes related to both virulence behaviour and the strain differences that have been relatively recently acquired from other sequence backgrounds. These frequently involve single genes or small numbers of genes that are not associated with transposases or bacteriophage genes, nor with inverted repeats typically used as markers for horizontal transfer. In addition, clear examples of horizontal exchange in genes associated with 'core' metabolic functions were identified, supported by differences between the sequenced strains, including: ftsK, xerD and polA. In some cases it was possible to determine which strain represented the 'parent' and 'altered' states for insertion-deletion events. Different signature component lengths showed different sensitivities for the detection of some horizontally transferred genes, which may reflect different amelioration rates of sequence components. Conclusion New implementations of signature analysis that can be applied on a gene-by-gene basis for the identification of horizontally acquired sequences are described. These findings highlight the central role of the availability of homologous substrates in evolution mediated by horizontal exchange, and suggest that some components of the supposedly stable 'core genome' may actually be favoured targets for integration of foreign sequences because of their degree of conservation

Both Virus and Host Components Are Important for the Manifestation of a Nef- Phenotype in HIV-1 and HIV-2

AbstractWhile it has been demonstrated that the Nef protein of simian immunodeficiency virus is obligatory for the establishment of high viral loads and the development of simian AIDS in rhesus macaques, demonstrating a critical role for the human immunodeficiency virus (HIV) Nef protein in tissue culture has been elusive. Data have been contradictory as to whether Nef has a negative or positive influence on in vitro virus replication. In an attempt to define a role for Nef during virus propagation in tissue culture and to obtain virus-host systems that could distinguish between the Nef mutant and wildtype viruses, we have introduced mutations into the nef genes of infectious molecular clones of three HIV-1 strains and two isolates of the HIV-2ROD strain and have investigated the capacity of viruses derived from them to infect a number of CD4-positive T-cell lines and peripheral blood mononuclear cells (PBMC). Mutating the nef gene of all viruses had a modest negative effect on virus production in activated PBMC. In some T-cell lines with some viruses, the effects were severe, and little or no Nef mutant virus could be detected. In other cell lines, the result of mutating the nef gene either had no effect or had a slight negative effect on the replication kinetics. Therefore, whether the consequences of loss of Nef activity can be demonstrated in vitro depends on both the particular virus and the host cell used, suggesting that Nef is exerting its activity on some cellular pathway. In addition, we describe the construction and properties of hitherto unreported infectious molecular clones of the ROD strain of HIV-2

Understanding Intra-Species and Inter-Species Prion Conversion and Zoonotic Potential Using Protein Misfolding Cyclic Amplification

Prion diseases are fatal neurodegenerative disorders that affect humans and animals, and can also be transmitted from animals to humans. A fundamental event in prion disease pathogenesis is the conversion of normal host prion protein (PrPC) to a disease-associated misfolded form (PrPSc). Whether or not an animal prion disease can infect humans cannot be determined a priori. There is a consensus that classical bovine spongiform encephalopathy (C-type BSE) in cattle transmits to humans, and that classical sheep scrapie is of little or no risk to human health. However, the zoonotic potential of more recently identified animal prion diseases, such as atypical scrapie, H-type and L-type BSE and chronic wasting disease (CWD) in cervids, remains an open question. Important components of the zoonotic barrier are (i) physiological differences between humans and the animal in question, (ii) amino acid sequence differences of the animal and human PrPC, and (iii) the animal prion strain, enciphered in the conformation of PrPSc. Historically, the direct inoculation of experimental animals has provided essential information on the transmissibility and compatibility of prion strains. More recently, cell-free molecular conversion assays have been used to examine the molecular compatibility on prion replication and zoonotic potential. One such assay is Protein Misfolding Cyclic Amplification (PMCA), in which a small amount of infected tissue homogenate, containing PrPSc, is added as a seed to an excess of normal tissue homogenate containing PrPC, and prion conversion is accelerated by cycles of incubation and ultrasonication. PMCA has been used to measure the molecular feasibility of prion transmission in a range of scenarios using genotypically homologous and heterologous combinations of PrPSc seed and PrPC substrate. Furthermore, this method can be used to speculate on the molecular profile of PrPSc that might arise from a zoonotic transmission. We discuss the experimental approaches that have been used to model both the intra- and inter-species molecular compatibility of prions, and the factors affecting PrPc to PrPSc conversion and zoonotic potential. We conclude that cell-free prion protein conversion assays, especially PMCA, are useful, rapid and low-cost approaches for elucidating the mechanisms of prion propagation and assessing the risk of animal prions to humans

Business Traveler Behavior after the Great Recession

The recent “Great Recession” prompted traditional business travelers to alter typical travel spending habits. One apparent behavioral change for travelers, highlighted in the Bureau of Labor Statistics consumer expenditure data, identified travelers’ tendency to buy significantly more groceries after the recession. This multiyear, longitudinal study revealed that business travelers doubled the consumption of grocery items after the recession as a possible means for alleviating non-subsidized food and beverage expenses. The employed business person, whose travel expenditures are wholly or partially subsidized by an employer, also appeared to drastically reduce personal travel expenditures for traditionally non-subsidized purchases. This study suggests that business travelers’ food consumption, tourism expenditures, length of stay and shopping behavior were affected by the recent recession. In addition, the responsible agents for the travelers in this study appeared to apply a conventional strategy for reducing the recession’s impact on the profit margin by reducing the length of the trips

The Impact of the Recent Recession Upon Tourism Behavior

The Labor Department’s 2012 report on consumer spending confirmed the recent recession forced consumers to alter the typical lifestyle spending habits. It’s apparent from the available consumer expenditure data that changes in the spending behavior for travelers dining choices continued beyond several years into the recovery period. In fact, the recorded decrease in food expenditures, from December 2007 to June 2009, was the largest inflation-adjusted amount ever recorded by the Bureau of Labor Statistics (BLS) since 1984. The increase in unemployment to 9.3% in 2009 was another important attribute of the consumers’ reduced spending levels during this recessionary period. According to the Food Expenditure Tables and the consumer Expenditure Survey U.S. household spending on food declined 5% between 2006 and 2009

Personal, social, and environmental factors associated with lifejacket wear in adults and children: A systematic literature review

Objective: Drowning claims 7% of the global burden of injury-related deaths. Lifejackets are routinely recommended as a drowning prevention strategy; however, a review of related factors regarding lifejacket wear has not previously been investigated. Methods: This systematic review examined literature published from inception to December 2016 in English and German languages. The personal, social, and environmental factors associated with lifejacket wear among adults and children were investigated, a quantitative evaluation of the results undertaken, and gaps in the literature identified. Results: Twenty studies, with sample sizes of studies ranging between 20 and 482,331, were identified. Fifty-five percent were cross-sectional studies. All studies were scored IV or V on the Australian National Health and Medical Research Council (NHMRC) grading system indicating mostly descriptive and cross-sectional levels of evidence. Factors associated with increased wear included age (mostly children), gender (mostly female), boat type (non-motorised), boat size (small boats), role modelling (children influenced by adult lifejacket wear), and activity (water-skiing, fishing). Factors not associated or inconsistent with lifejacket wear included education, household income, ethnicity, boating ability, confidence in lifejackets, waterway type, and weather and water conditions. Factors associated with reduced lifejacket wear included adults, males, discomfort, cost and accessibility, consumption of alcohol, and swimming ability. Three studies evaluated the impact of interventions. Conclusion: This review identified factors associated with both increased and decreased lifejacket wear. Future research should address the motivational factors associated with individuals’ decisions to wear or not wear lifejackets. This, combined with further research on the evaluation of interventions designed to increase lifejacket wear, will enhance the evidence base to support future drowning prevention interventions

Anomalous Behavior of Ru for Catalytic Oxidation: A Theoretical Study of the Catalytic Reaction CO + 1/2 O_2 --> CO_2

Recent experiments revealed an anomalous dependence of carbon monoxide oxidation at Ru(0001) on oxygen pressure and a particularly high reaction rate. Below we report density functional theory calculations of the energetics and reaction pathways of the speculated mechanism. We will show that the exceptionally high rate is actuated by a weakly but nevertheless well bound (1x1) oxygen adsorbate layer. Furthermore it is found that reactions via scattering of gas-phase CO at the oxygen covered surface may play an important role. Our analysis reveals, however, that reactions via adsorbed CO molecules (the so-called Langmuir-Hinshelwood mechanism) dominate.Comment: 5 pages, 4 figures, Phys. Rev. Letters, Feb. 1997, in prin