Linewidths in bound state resonances for helium scattering from Si(111)-(1x1)H

Helium-3 spin-echo measurements of resonant scattering from the Si(111)–(1 × 1)H surface, in the energy range 4–14 meV, are presented. The measurements have high energy resolution yet they reveal bound state resonance features with uniformly broad linewidths. We show that exact quantum mechanical calculations of the elastic scattering, using the existing potential for the helium/Si(111)–(1 × 1)H interaction, cannot reproduce the linewidths seen in the experiment. Further calculations rule out inelastic and other mechanisms that might give rise to losses from the elastic scattering channels. We show that corrugation in the attractive part of the atom–surface potential is the most likely origin of the experimental lineshapes

Weak intermolecular interactions in an ionically bound molecular adsorbate: cyclopentadienyl=Cu(111)

The dissociative adsorption of cyclopentadiene (C5H6) on Cu(111) yields a cyclopentadienyl (Cp) species with strongly anionic characteristics. The Cp potential energy surface and frictional coupling to the substrate are determined from measurements of dynamics of the molecule together with density functional calculations. The molecule is shown to occupy degenerate threefold adsorption sites and molecular motion is characterized by a low diffusional energy barrier of 40 +/- 3 meV with strong frictional dissipation. Repulsive dipole-dipole interactions are not detected despite charge transfer from substrate to adsorbate

Cytomegalovirus microRNAs Facilitate Persistent Virus Infection in Salivary Glands

Micro (mi)RNAs are small non-coding RNAs that regulate the expression of their targets' messenger RNAs through both translational inhibition and regulation of target RNA stability. Recently, a number of viruses, particularly of the herpesvirus family, have been shown to express their own miRNAs to control both viral and cellular transcripts. Although some targets of viral miRNAs are known, their function in a physiologically relevant infection remains to be elucidated. As such, no in vivo phenotype of a viral miRNA knock-out mutant has been described so far. Here, we report on the first functional phenotype of a miRNA knock-out virus in vivo. During subacute infection of a mutant mouse cytomegalovirus lacking two viral miRNAs, virus production is selectively reduced in salivary glands, an organ essential for virus persistence and horizontal transmission. This phenotype depends on several parameters including viral load and mouse genetic background, and is abolished by combined but not single depletion of natural killer (NK) and CD4+ T cells. Together, our results point towards a miRNA-based immunoevasion mechanism important for long-term virus persistence

Pre-Micro RNA Signatures Delineate Stages of Endothelial Cell Transformation in Kaposi Sarcoma

MicroRNAs (miRNA) have emerged as key regulators of cell lineage differentiation and cancer. We used precursor miRNA profiling by a novel real-time QPCR method (i) to define progressive stages of endothelial cell transformation cumulating in Kaposi sarcoma (KS) and (ii) to identify specific miRNAs that serve as biomarkers for tumor progression. We were able to compare primary patient biopsies to well-established culture and mouse tumor models. Loss of mir-221 and gain of mir-15 expression demarked the transition from merely immortalized to fully tumorigenic endothelial cells. Mir-140 and Kaposi sarcoma–associated herpesvirus viral miRNAs increased linearly with the degree of transformation. Mir-24 emerged as a biomarker specific for KS

The Cardiac Transcription Network Modulated by Gata4, Mef2a, Nkx2.5, Srf, Histone Modifications, and MicroRNAs

The transcriptome, as the pool of all transcribed elements in a given cell, is regulated by the interaction between different molecular levels, involving epigenetic, transcriptional, and post-transcriptional mechanisms. However, many previous studies investigated each of these levels individually, and little is known about their interdependency. We present a systems biology study integrating mRNA profiles with DNA–binding events of key cardiac transcription factors (Gata4, Mef2a, Nkx2.5, and Srf), activating histone modifications (H3ac, H4ac, H3K4me2, and H3K4me3), and microRNA profiles obtained in wild-type and RNAi–mediated knockdown. Finally, we confirmed conclusions primarily obtained in cardiomyocyte cell culture in a time-course of cardiac maturation in mouse around birth. We provide insights into the combinatorial regulation by cardiac transcription factors and show that they can partially compensate each other's function. Genes regulated by multiple transcription factors are less likely differentially expressed in RNAi knockdown of one respective factor. In addition to the analysis of the individual transcription factors, we found that histone 3 acetylation correlates with Srf- and Gata4-dependent gene expression and is complementarily reduced in cardiac Srf knockdown. Further, we found that altered microRNA expression in Srf knockdown potentially explains up to 45% of indirect mRNA targets. Considering all three levels of regulation, we present an Srf-centered transcription network providing on a single-gene level insights into the regulatory circuits establishing respective mRNA profiles. In summary, we show the combinatorial contribution of four DNA–binding transcription factors in regulating the cardiac transcriptome and provide evidence that histone modifications and microRNAs modulate their functional consequence. This opens a new perspective to understand heart development and the complexity cardiovascular disorders

Systematic MicroRNA Analysis Identifies ATP6V0C as an Essential Host Factor for Human Cytomegalovirus Replication

Recent advances in microRNA target identification have greatly increased the number of putative targets of viral microRNAs. However, it is still unclear whether all targets identified are biologically relevant. Here, we use a combined approach of RISC immunoprecipitation and focused siRNA screening to identify targets of HCMV encoded human cytomegalovirus that play an important role in the biology of the virus. Using both a laboratory and clinical strain of human cytomegalovirus, we identify over 200 putative targets of human cytomegalovirus microRNAs following infection of fibroblast cells. By comparing RISC-IP profiles of miRNA knockout viruses, we have resolved specific interactions between human cytomegalovirus miRNAs and the top candidate target transcripts and validated regulation by western blot analysis and luciferase assay. Crucially we demonstrate that miRNA target genes play important roles in the biology of human cytomegalovirus as siRNA knockdown results in marked effects on virus replication. The most striking phenotype followed knockdown of the top target ATP6V0C, which is required for endosomal acidification. siRNA knockdown of ATP6V0C resulted in almost complete loss of infectious virus production, suggesting that an HCMV microRNA targets a crucial cellular factor required for virus replication. This study greatly increases the number of identified targets of human cytomegalovirus microRNAs and demonstrates the effective use of combined miRNA target identification and focused siRNA screening for identifying novel host virus interactions

Bayesian Analysis of Curves Shape Variation Through Registration and Regression

This manuscript reviews the use of Bayesian hierarchical curve registration in Biostatistics and Bioinformatics.Several models allowing for unit-specific random time scales are discussed and applied to longitudinal dataarising in biomedicine, pharmacokinetics and time-course genomics. We consider representations of random functionals based on P-spline priors. Under this framework, straightforward posterior simulation strategies are outlined for inference.Beyond curve registration, we discuss jointregression modeling of both random effects and population level functional quantities. Finally, the use of mixture priors is discussed in the setting of differential expression analysis

Is Happiness a trait?

ABSTRACT One of the ideological foundations of the modern welfare states is the belief that people can be made happier by providing them with better living conditions. This belief is challenged by the theory that happiness is a fixed 'trait', rather than a variable 'state'. This theory figures both at the individual level and at the societal level. The individual level variant depicts happiness as an aspect of personal character; rooted in inborn temperament or acquired disposition. The societal variant sees happiness as a matter of national character; embedded in shared values and beliefs. Both variants imply that a better society makes no happier people. Happiness can be regarded as a trait if it meets three criteria: 1) temporal stability, 2) cross-situational consistency, and 3) inner causation. This paper checks whether that is, indeed, the case. The theory that happiness is a personal-character-trait is tested in a (meta) analysis of longitudinal studies. The results are: 1) Happiness is quite stable on the short term, but not in the long run, neither relatively nor absoloutely. 2) Happiness is not insensitive to fortune or adversity. 3) Happiness is not entirely built-in: its genetic basis is at best modest and psychological factors explain only part of its variance. The theory that happiness is a national-character-trait is tested in an analysis of differences in average happiness between nations. The results point in the same direction: 1) Though generally fairly stable over the last decades, nation-happiness has changed profoundly in some cases both absolutely and relatively. 2) Average happiness in nations is clearly not indep