Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12.

IHF and HU are two heterodimeric nucleoid-associated proteins (NAP) that belong to the same protein family but interact differently with the DNA. IHF is a sequence-specific DNA-binding protein that bends the DNA by over 160°. HU is the most conserved NAP, which binds non-specifically to duplex DNA with a particular preference for targeting nicked and bent DNA. Despite their importance, the in vivo interactions of the two proteins to the DNA remain to be described at a high resolution and on a genome-wide scale. Further, the effects of these proteins on gene expression on a global scale remain contentious. Finally, the contrast between the functions of the homo- and heterodimeric forms of proteins deserves the attention of further study. Here we present a genome-scale study of HU- and IHF binding to the Escherichia coli K12 chromosome using ChIP-seq. We also perform microarray analysis of gene expression in single- and double-deletion mutants of each protein to identify their regulons. The sequence-specific binding profile of IHF encompasses ∼30% of all operons, though the expression of <10% of these is affected by its deletion suggesting combinatorial control or a molecular backup. The binding profile for HU is reflective of relatively non-specific binding to the chromosome, however, with a preference for A/T-rich DNA. The HU regulon comprises highly conserved genes including those that are essential and possibly supercoiling sensitive. Finally, by performing ChIP-seq experiments, where possible, of each subunit of IHF and HU in the absence of the other subunit, we define genome-wide maps of DNA binding of the proteins in their hetero- and homodimeric forms

Predictors of Employee Involvement in a Worksite Health Promotion Program

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/67001/2/10.1177_109019819001700404.pd

Phosphorylation of the androgen receptor is associated with reduced survival in hormonerefractory prostate cancer patients

Cell line studies demonstrate that the PI3K/Akt pathway is upregulated in hormone-refractory prostate cancer (HRPC) and can result in phosphorylation of the androgen receptor (AR). The current study therefore aims to establish if this has relevance to the development of clinical HRPC. Immunohistochemistry was employed to investigate the expression and phosphorylation status of Akt and AR in matched hormone-sensitive and -refractory prostate cancer tumours from 68 patients. In the hormone-refractory tissue, only phosphorylated AR (pAR) was associated with shorter time to death from relapse (&lt;i&gt;P&lt;/i&gt;=0.003). However, when an increase in expression in the transition from hormone-sensitive to -refractory prostate cancer was investigated, an increase in expression of PI3K was associated with decreased time to biochemical relapse (&lt;i&gt;P&lt;/i&gt;=0.014), and an increase in expression of pAkt&lt;sup&gt;473&lt;/sup&gt; and pAR&lt;sup&gt;210&lt;/sup&gt; were associated with decreased disease-specific survival (&lt;i&gt;P&lt;/i&gt;=0.0019 and 0.0015, respectively). Protein expression of pAkt&lt;sup&gt;473&lt;/sup&gt; and pAR&lt;sup&gt;210&lt;/sup&gt; also strongly correlated (&lt;i&gt;P&lt;/i&gt;&#60;0.001, c.c.=0.711) in the hormone-refractory prostate tumours. These results provide evidence using clinical specimens, that upregulation of the PI3K/Akt pathway is associated with phosphorylation of the AR during development of HRPC, suggesting that this pathway could be a potential therapeutic target

Struggles over access to the Muslim public sphere: Multiple publics and discourses on agency, belonging and citizenship (Introduction to the Themed Section)

Abstract This introductory essay provides the context for the articles in this Themed Section. Despite the diversity in locations, historical backgrounds and contemporary processes of change, all contributors to this Themed Section focus on the struggle of Muslim groups over access to an emergent Muslim public sphere. They highlight the contestations of and shifts in the notions of agency, belonging, and citizenship in nation-states with Muslim communities within its borders. The introduction consists of two parts. The first part reviews the notion of the public sphere as conceptualized by Habermas and critiqued by scholars of a diversity of backgrounds. In relation to the concept of the Muslim public sphere, three aspects of critique are given closer c

Modelling a response as a function of high frequency count data: the association between physical activity and fat mass

We present a new statistical modelling approach where the response is a function of high frequency count data. Our application is about investigating the relationship between the health outcome fat mass and physical activity (PA) measured by accelerometer. The accelerometer quantifies the intensity of physical activity as counts per epoch over a given period of time. We use data from the Avon longitudinal study of parents and children (ALSPAC) where accelerometer data is available as a time series of accelerometer counts per minute over seven days for a subset of children. In order to compare accelerometer profiles between individuals and to reduce the high dimension a functional summary of the profiles is used. We use the histogram as a functional summary due to its simplicity, suitability and ease of interpretation. Our model is an extension of generalised regression of scalars on functions or signal regression. It allows also multi-dimensional functional predictors and additive non-linear predictors for metric covariates. The additive multidimensional functional predictors allow investigating specific questions about whether the effect of PA varies over its intensity, by gender, by time of day or by day of the week. The key feature of the model is that it utilises the full profile of measured PA without requiring cut-points defining intensity levels for light, moderate and vigorous activity. We show that the (not necessarily causal) effect of PA is not linear and not constant over the activity intensity. Also, there is little evidence to suggest that the effect of PA intensity varies by gender or whether it happens on weekdays or on weekends

Calculating the potential for within-flight transmission of influenza A (H1N1)

Abstract Background Clearly air travel, by transporting infectious individuals from one geographic location to another, significantly affects the rate of spread of influenza A (H1N1). However, the possibility of within-flight transmission of H1N1 has not been evaluated; although it is known that smallpox, measles, tuberculosis, SARS and seasonal influenza can be transmitted during commercial flights. Here we present the first quantitative risk assessment to assess the potential for within-flight transmission of H1N1. Methods We model airborne transmission of infectious viral particles of H1N1 within a Boeing 747 using methodology from the field of quantitative microbial risk assessment. Results The risk of catching H1N1 will essentially be confined to passengers travelling in the same cabin as the source case. Not surprisingly, we find that the longer the flight the greater the number of infections that can be expected. We calculate that H1N1, even during long flights, poses a low to moderate within-flight transmission risk if the source case travels First Class. Specifically, 0-1 infections could occur during a 5 hour flight, 1-3 during an 11 hour flight and 2-5 during a 17 hour flight. However, within-flight transmission could be significant, particularly during long flights, if the source case travels in Economy Class. Specifically, two to five infections could occur during a 5 hour flight, 5-10 during an 11 hour flight and 7-17 during a 17 hour flight. If the aircraft is only partially loaded, under certain conditions more infections could occur in First Class than in Economy Class. During a 17 hour flight, a greater number of infections would occur in First Class than in Economy if the First Class Cabin is fully occupied, but Economy class is less than 30% full. Conclusions Our results provide insights into the potential utility of air travel restrictions on controlling influenza pandemics in the winter of 2009/2010. They show travel by one infectious individual, rather than causing a single outbreak of H1N1, could cause several simultaneous outbreaks. These results imply that, during a pandemic, quarantining passengers who travel in Economy on long-haul flights could potentially be an important control strategy. Notably, our results show that quarantining passengers who travel First Class would be unlikely to be an effective control strategy

Protective role of vitamin B6 (PLP) against DNA damage in Drosophila models of type 2 diabetes

Growing evidence shows that improper intake of vitamin B6 increases cancer risk and several studies indicate that diabetic patients have a higher risk of developing tumors. We previously demonstrated that in Drosophila the deficiency of Pyridoxal 5' phosphate (PLP), the active form of vitamin B6, causes chromosome aberrations (CABs), one of cancer prerequisites, and increases hemolymph glucose content. Starting from these data we asked if it was possible to provide a link between the aforementioned studies. Thus, we tested the effect of low PLP levels on DNA integrity in diabetic cells. To this aim we generated two Drosophila models of type 2 diabetes, the first by impairing insulin signaling and the second by rearing flies in high sugar diet. We showed that glucose treatment induced CABs in diabetic individuals but not in controls. More interestingly, PLP deficiency caused high frequencies of CABs in both diabetic models demonstrating that hyperglycemia, combined to reduced PLP level, impairs DNA integrity. PLP-depleted diabetic cells accumulated Advanced Glycation End products (AGEs) that largely contribute to CABs as α-lipoic acid, an AGE inhibitor, rescued not only AGEs but also CABs. These data, extrapolated to humans, indicate that low PLP levels, impacting on DNA integrity, may be considered one of the possible links between diabetes and cancer

Electronic nature of the enhanced conductivity in YSZ-STO multilayers deposited by PLD

10 páginas, 8 figuras.-- et al.The search for new strategies to enhance the oxide ionic conductivity in oxide materials is a very active field of research. These materials are needed for application in a new generation of more efficient and durable solid state electrochemical devices such as reduced-temperature Solid Oxide Fuel Cells (SOFC's). Recently published results have claimed that sputtered yttria stabilised zirconia (YSZ)/SrTiO3 (STO) heterostructures show enhanced oxygen ion conductivity, by about eight orders of magnitude, with respect to that expected for YSZ and STO bulk values. The YSZ/STO heterostructures obtained in this work from Pulsed Laser Deposited (PLD) films, also show enhanced conductivity of a similar order. However, the fact that our structures show different relative orientations indicates that the conductivity enhancement may not be associated to a particular crystallographic arrangement at the interface. The combined characterisation of the conductivity dependence on oxygen partial pressure and direct oxygen diffusion by means of tracer experiments clearly demonstrate that the enhancement observed is related to the electronic rather than ionic conductivity.The authors also acknowledge the financial support of Spanish Government through projects: MAT2008-04931 and Consolider-Ingenio 2010-CSD2008-023. Two of the authors (A.C. and M.B.) acknowledge the support of their postdoctoral fellowships from the Spanish Ministry of Science and Innovation. DWM acknowledges the support of the Royal Academy of Engineering.Peer reviewe

Anomalous Oxidation States in Multilayers for Fuel Cell Applications

Significant recent interest has been directed towards the relationship between interfaces and reports of enhanced ionic conductivity. To gain a greater understanding of the effects of hetero-interfaces on ionic conductivity, advanced analytical techniques including electron microscopy (TEM/STEM), electron energy loss spectroscopy (EELS), and secondary ion mass spectrometry (SIMS) are used to characterize CeO2/Ce0.85Sm0.15O2 multilayer thin films grown by pulsed laser deposition. High quality growth is observed, but ionic conductivity measured by impedance spectroscopy and O-18 tracer experiments is consistent with bulk materials. EELS analysis reveals the unusual situation of layers containing only Ce(IV) adjacent to layers containing both Ce(III) and Ce(IV). Post oxygen annealing induced oxygen diffusion and mixed oxidation states in both layers, but only in the vicinity of low angle grain boundaries perpendicular to the layers. The implications of the anomalous behavior of the Ce oxidation states on the design of novel electrolytes for solid oxide fuel cells is discussed