Transcriptome Analyses of Tumor-Adjacent Somatic Tissues Reveal Genes Co-Expressed with Transposable Elements

Background: Despite the long-held assumption that transposons are normally only expressed in the germ-line, recent evidence shows that transcripts of transposable element (TE) sequences are frequently found in the somatic cells. However, the extent of variation in TE transcript levels across different tissues and different individuals are unknown, and the co-expression between TEs and host gene mRNAs have not been examined. Results: Here we report the variation in TE derived transcript levels across tissues and between individuals observed in the non-tumorous tissues collected for The Cancer Genome Atlas. We found core TE co-expression modules consisting mainly of transposons, showing correlated expression across broad classes of TEs. Despite this co-expression within tissues, there are individual TE loci that exhibit tissue-specific expression patterns, when compared across tissues. The core TE modules were negatively correlated with other gene modules that consisted of immune response genes in interferon signaling. KRAB Zinc Finger Proteins (KZFPs) were over-represented gene members of the TE modules, showing positive correlation across multiple tissues. But we did not find overlap between TE-KZFP pairs that are co-expressed and TE-KZFP pairs that are bound in published ChIP-seq studies. Conclusions: We find unexpected variation in TE derived transcripts, within and across non-tumorous tissues. We describe a broad view of the RNA state for non-tumorous tissues exhibiting higher level of TE transcripts. Tissues with higher level of TE transcripts have a broad range of TEs co-expressed, with high expression of a large number of KZFPs, and lower RNA levels of immune genes

Monte Carlo Simulations of Globular Cluster Evolution - II. Mass Spectra, Stellar Evolution and Lifetimes in the Galaxy

We study the dynamical evolution of globular clusters using our new 2-D Monte Carlo code, and we calculate the lifetimes of clusters in the Galactic environment. We include the effects of a mass spectrum, mass loss in the Galactic tidal field, and stellar evolution. We consider initial King models containing N = 10^5 - 3x10^5 stars, and follow the evolution up to core collapse, or disruption, whichever occurs first. We find that the lifetimes of our models are significantly longer than those obtained using 1-D Fokker-Planck (F-P) methods. We also find that our results are in very good agreement with recent 2-D F-P calculations, for a wide range of initial conditions. Our results show that the direct mass loss due to stellar evolution can significantly accelerate the mass loss through the tidal boundary, causing most clusters with a low initial central concentration (Wo <~ 3) to disrupt quickly in the Galactic tidal field. Only clusters born with high initial central concentrations (Wo >~ 7) or steep initial mass functions are likely to survive to the present and undergo core collapse. We also study the orbital characteristics of escaping stars, and find that the velocity distribution of escaping stars in collapsing clusters looks significantly different from the distribution in disrupting clusters. We calculate the lifetime of a cluster on an eccentric orbit in the Galaxy, such that it fills its Roche lobe only at perigalacticon. We find that such an orbit can extend the lifetime by at most a factor of a few compared to a circular orbit in which the cluster fills its Roche lobe at all times.Comment: 32 pages, including 10 figures, to appear in ApJ, minor corrections onl

Six Recital Pieces for Percussion

This paper provides information on six recital pieces written by some of the leading composers in today\u27s percussion repertoire. Those included are James Campbell\u27s Tangents, Javier Álvarez\u27s Temazcal, Keiko Abe\u27s Prism Rhapsody for Marimba and Orchestra, Michio Kitazume\u27s Side by Side, Christopher Norton\u27s Summer Daybreak, and Chad Floyd\u27s Triptych Boom. Many topics are discussed, including composer biographies, historical significance, theory, analysis, and performance practice

East Bay Coalition for the Homeless: Branding Study and Marketing Strategy

There are a number of potential positioning strategies. The two which make the most sense for the EBCH are to “position the EBCH away from others in the category” and to “position the EBCH as unique.” These strategies have the advantage of setting the EBCH apart from the other organizations that address homelessness. Occupying its own “position” in the minds of potential and current donors is not only an effective communications/marketing strategy but also a less costly one because it avoids head-to-head competition and comparisons

Little evidence that nonmonogamous family structures are detrimental to childrens well-being in Mpimbwe, Tanzania.

Nuclear family structures are often thought to be essential for the well-being of children. Divorce, the loss of either biological parent, the presence of step-parents, and the practice of polygynous marriage have all been claimed to negatively impact child well-being. However, empirical research on these topics has been limited by the routine use of cross-regional and cross-sectional databases. Cross-regional data render research vulnerable to the ecological inference fallacy, and cross-sectional data prevent assessment of age-specific impacts of time-varying family-structure variables. When longitudinal data are available, they tend to be drawn from Western/urban contexts. Detailed data on family structure and childrens well-being are rarely collected in more marginalized communities. In many rural and traditional communities, nonnuclear family structures are indeed prevalent and viewed as socially permissible-and, as such, may have different impacts on childrens well-being than in Western contexts. Here, we draw on a detailed, longitudinal dataset from a 20-y prospective study in rural Tanzania, where polygyny and serial monogamy are common. We analyze survival outcomes for 3,693 children born between 1931 and 2014, growth outcomes for 881 children born between 1976 and 2014, and educational outcomes for 1,370 children born between 1976 and 2014. Our analyses indicate that monogamous marriage is not consistently associated with better outcomes for children-contrary to some popular and public health perspectives on human family structure

A gene–culture co-evolutionary perspective on the puzzle of human twinship

Natural selection should favour litter sizes that optimise trade-offs between brood-size and offspring viability. Across the primate order, the modal litter size is one, suggesting a deep history of selection favouring minimal litters in primates. Humans, however – despite having the longest juvenile period and slowest life-history of all primates – still produce twin births at appreciable rates, even though such births are costly. This presents an evolutionary puzzle. Why is twinning still expressed in humans despite its cost? More puzzling still is the discordance between the principal explanations for human twinning and extant empirical data. Such explanations propose that twinning is regulated by phenotypic plasticity in polyovulation, permitting the production of larger sib sets if and when resources are abundant. However, comparative data suggest that twinning rates are actually highest in poorer economies and lowest in richer, more developed economies. We propose that a historical dynamic of gene–culture co-evolution might better explain this geographic patterning. Our explanation distinguishes geminophilous and geminophobic cultural contexts, as those celebrating twins (e.g. through material support) and those hostile to twins (e.g. through sanction of twin-infanticide). Geminophilous institutions, in particular, may buffer the fitness cost associated with twinning, potentially reducing selection pressures against polyovulation. We conclude by synthesising a mathematical and empirical research programme that might test our ideas.</p

Leveraging University Partnerships to Build Capacity in Rural Schools: A Case Study

University partnerships provide an avenue to increase capacity within K-12 schools. This case study reviews and successful partnership and the steps taken to make it work