Numerical study of scars in a chaotic billiard

We study numerically the scaling properties of scars in stadium billiard. Using the semiclassical criterion, we have searched systematically the scars of the same type through a very wide range, from ground state to as high as the 1 millionth state. We have analyzed the integrated probability density along the periodic orbit. The numerical results confirm that the average intensity of certain types of scars is independent of $\hbar$ rather than scales with $\sqrt{\hbar}$. Our findings confirm the theoretical predictions of Robnik (1989).Comment: 7 pages in Revtex 3.1, 5 PS figures available upon request. To appear in Phys. Rev. E, Vol. 55, No. 5, 199

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.

Analysis of DNA methylation patterns relies increasingly on sequencing-based profiling methods. The four most frequently used sequencing-based technologies are the bisulfite-based methods MethylC-seq and reduced representation bisulfite sequencing (RRBS), and the enrichment-based techniques methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylated DNA binding domain sequencing (MBD-seq). We applied all four methods to biological replicates of human embryonic stem cells to assess their genome-wide CpG coverage, resolution, cost, concordance and the influence of CpG density and genomic context. The methylation levels assessed by the two bisulfite methods were concordant (their difference did not exceed a given threshold) for 82% for CpGs and 99% of the non-CpG cytosines. Using binary methylation calls, the two enrichment methods were 99% concordant and regions assessed by all four methods were 97% concordant. We combined MeDIP-seq with methylation-sensitive restriction enzyme (MRE-seq) sequencing for comprehensive methylome coverage at lower cost. This, along with RNA-seq and ChIP-seq of the ES cells enabled us to detect regions with allele-specific epigenetic states, identifying most known imprinted regions and new loci with monoallelic epigenetic marks and monoallelic expression

A realistic example of chaotic tunneling: The hydrogen atom in parallel static electric and magnetic fields

Statistics of tunneling rates in the presence of chaotic classical dynamics is discussed on a realistic example: a hydrogen atom placed in parallel uniform static electric and magnetic fields, where tunneling is followed by ionization along the fields direction. Depending on the magnetic quantum number, one may observe either a standard Porter-Thomas distribution of tunneling rates or, for strong scarring by a periodic orbit parallel to the external fields, strong deviations from it. For the latter case, a simple model based on random matrix theory gives the correct distribution.Comment: Submitted to Phys. Rev.

Surface-Enhanced Nitrate Photolysis on Ice

Heterogeneous nitrates photolysis is the trigger for many chemical processes occurring in the polar boundary layer and is widely believed to occur in a quasi-liquid layer (QLL) at the surface of ice. The dipole forbidden character of the electronic transition relevant to boundary layer atmospheric chemistry and the small photolysis/photoproducts quantum yields in ice (and in water) may confer a significant enhancement and interfacial specificity to this important photochemical reaction at the surface of ice. Using amorphous solid water films at cryogenic temperatures as models for the disordered interstitial air/ice interface within the snowpack suppresses the diffusive uptake kinetics thereby prolonging the residence time of nitrate anions at the surface of ice. This approach allows their slow heterogeneous photolysis kinetics to be studied providing the first direct evidence that nitrates adsorbed onto the first molecular layer at the surface of ice are photolyzed more effectively than those dissolved within the bulk. Vibrational spectroscopy allows the ~3-fold enhancement in photolysis rates to be correlated with the nitrates’ distorted intramolecular geometry thereby hinting at the role played by the greater chemical heterogeneity in their solvation environment at the surface of ice than in the bulk. A simple 1D kinetic model suggests 1-that a 3(6)-fold enhancement in photolysis rate for nitrates adsorbed onto the ice surface could increase the photochemical NO[subscript 2] emissions from a 5(8) nm thick photochemically active interfacial layer by 30%(60)%, and 2-that 25%(40%) of the NO[subscript 2] photochemical emissions to the snowpack interstitial air are released from the top-most molecularly thin surface layer on ice. These findings may provide a new paradigm for heterogeneous (photo)chemistry at temperatures below those required for a QLL to form at the ice surface

Early influences on cardiovascular and renal development

The hypothesis that a developmental component plays a role in subsequent disease initially arose from epidemiological studies relating birth size to both risk factors for cardiovascular disease and actual cardiovascular disease prevalence in later life. The findings that small size at birth is associated with an increased risk of cardiovascular disease have led to concerns about the effect size and the causality of the associations. However, recent studies have overcome most methodological flaws and suggested small effect sizes for these associations for the individual, but an potential important effect size on a population level. Various mechanisms underlying these associations have been hypothesized, including fetal undernutrition, genetic susceptibility and postnatal accelerated growth. The specific adverse exposures in fetal and early postnatal life leading to cardiovascular disease in adult life are not yet fully understood. Current studies suggest that both environmental and genetic factors in various periods of life may underlie the complex associations of fetal growth retardation and low birth weight with cardiovascular disease in later life. To estimate the population effect size and to identify the underlying mechanisms, well-designed epidemiological studies are needed. This review is focused on specific adverse fetal exposures, cardiovascular adaptations and perspectives for new studies. Copyrigh

Extending Epigenesis: From Phenotypic Plasticity to the Bio-Cultural Feedback

The paper aims at proposing an extended notion of epigenesis acknowledging an actual causal import to the phenotypic dimension for the evolutionary diversification of life forms. Section 1 offers introductory remarks on the issue of epigenesis contrasting it with ancient and modern preformationist views. In Section 2 we propose to intend epigenesis as a process of phenotypic formation and diversification a) dependent on environmental influences, b) independent of changes in the genomic nucleotide sequence, and c) occurring during the whole life span. Then, Section 3 focuses on phenotypic plasticity and offers an overview of basic properties (like robustness, modularity and degeneracy) that allows biological systems to be evolvable – i.e. to have the potentiality of producing phenotypic variation. Successively (Section 4), the emphasis is put on environmentally-induced modification in the regulation of gene expression giving rise to phenotypic variation and diversification. After some brief considerations on the debated issue of epigenetic inheritance (Section 5), the issue of culture (kept in the background of the preceding sections) is considered. The key point is that, in the case of humans and of the evolutionary history of the genus Homo at least, the environment is also, importantly, the cultural environment. Thus, Section 6 argues that a bio-cultural feedback should be acknowledged in the “epigenic” processes leading to phenotypic diversification and innovation in Homo evolution. Finally, Section 7 introduces the notion of “cultural neural reuse”, which refers to phenotypic/neural modifications induced by specific features of the cultural environment that are effective in human cultural evolution without involving genetic changes. Therefore, cultural neural reuse may be regarded as a key instance of the bio-cultural feedback and ultimately of the extended notion of epigenesis proposed in this work

Genome-wide DNA methylation map of human neutrophils reveals widespread inter-individual epigenetic variation

The extent of variation in DNA methylation patterns in healthy individuals is not yet well documented. Identification of inter-individual epigenetic variation is important for understanding phenotypic variation and disease susceptibility. Using neutrophils from a cohort of healthy individuals, we generated base-resolution DNA methylation maps to document inter-individual epigenetic variation. We identified 12851 autosomal inter-individual variably methylated fragments (iVMFs). Gene promoters were the least variable, whereas gene body and upstream regions showed higher variation in DNA methylation. The iVMFs were relatively enriched in repetitive elements compared to non-iVMFs, and were associated with genome regulation and chromatin function elements. Further, variably methylated genes were disproportionately associated with regulation of transcription, responsive function and signal transduction pathways. Transcriptome analysis indicates that iVMF methylation at differentially expressed exons has a positive correlation and local effect on the inclusion of that exon in the mRNA transcript

Environmental chemical stressors as epigenome modifiers:a new horizon in assessment of toxicological effects

In eukaryotic cells, chromatin transformation from euchromatin into heterochromatin as a means of controlling gene expression and replication has been known as the ?accessibility hypothesis?. The interplay of epigenetic changes including histone modifications, DNA methylation, RNA interference (RNAi) and other functional epigenetic components are intricate. It is believed that these changes are well-programmed, inherited and can be modified by environmental contaminant stressors. Environmentally-driven epigenetic alterations during development, e.g. embryonic, foetal or neonatal stage, may influence disease susceptibility in adulthood. Therefore, understanding how epigenome modifications develop in response to environmental chemicals and, how epigenetic-xenobiotic interactions influence human health will shed new insights into gene-environment interactions in the epidemiology of several diseases including cancer. In this review, we consider studies of chemical modifiers including nutritional and xenobiotic effects on epigenetic components in vitro or in vivo. By examining the most-studied epigenome modifications and how their respective roles are interlinked, we highlight the central role of xenbiotic-modified epigenetic mechanisms. A major requirement will be to study and understand effects following environmentally-relevant exposures. We suggest that the study of epigenetic toxicology will open up new opportunities to devise strategies for the prevention or treatment of at-risk populations

Sensitivity to situated positionings: Generating insight into organizational change

Within ethnographic forms of organisational research, sensitivity to context is generally acknowledged as a critical ingredient for analysing processes and practices. When conducting such research, however, researchers typically privilege one particular research context for generating knowledge: although some ethnographic scholars underscore the importance of adopting a diversity of both insider and outsider roles, ethnographic research is usually equated with gaining a deep familiarity with the field of study through immersion. First, we argue that, although immersion elicits valuable knowledge ‘from within’, its prioritisation inevitably blinds the researcher’s eye to equally interesting insights stemming from alternative – and often unintended – positionings. Testifying to the significance of researchers’ relational reflexivity for data interpretation, we show how a variety of researcher’ positionings vis-à-vis the researched generated a variety of insights. Critical sensitivity to fieldworker identities in an ethnographic study of planned organisational change within a police organisation allowed us, second, to criticise the change management literature for routinely building on a fixed dichotomy between ‘change agents’ and ‘change recipients’ and to empirically demonstrate a wider variety of police officers’ positionings in relation to change initiatives (i.e. countering, complying with and co-opting) and its initiators (i.e. engaging in other-depreciating, self-questioning or self-affirming identity work)