Assembly Bias of Dwarf-sized Dark Matter Haloes

Previous studies indicate that assembly bias effects are stronger for lower mass dark matter haloes. Here we make use of high resolution re-simulations of rich clusters and their surroundings from the Phoenix Project and a large volume cosmological simulation, the Millennium-II run, to quantify assembly bias effects on dwarf-sized dark matter haloes. We find that, in the regions around massive clusters, dwarf-sized haloes ([10^9,10^{11}]\ms) form earlier ($\Delta z \sim 2$ in redshift) and possess larger $V_{\rm max}$ ($\sim20$) than the field galaxies. We find that this environmental dependence is largely caused by tidal interactions between the ejected haloes and their former hosts, while other large scale effects are less important. Finally we assess the effects of assembly bias on dwarf galaxy formation with a sophisticated semi-analytical galaxy formation model. We find that the dwarf galaxies near massive clusters tend to be redder ($\Delta(u-r) = 0.5$) and have three times as much stellar mass compared to the field galaxies with the same halo mass. These features should be seen with observational data.Comment: 8 pages, 8 figures, accepted by MNRA

Long terminal repeat retrotransposons of Oryza sativa

BACKGROUND: Long terminal repeat (LTR) retrotransposons constitute a major fraction of the genomes of higher plants. For example, retrotransposons comprise more than 50% of the maize genome and more than 90% of the wheat genome. LTR retrotransposons are believed to have contributed significantly to the evolution of genome structure and function. The genome sequencing of selected experimental and agriculturally important species is providing an unprecedented opportunity to view the patterns of variation existing among the entire complement of retrotransposons in complete genomes. RESULTS: Using a new data-mining program, LTR_STRUC, (LTR retrotransposon structure program), we have mined the GenBank rice (Oryza sativa) database as well as the more extensive (259 Mb) Monsanto rice dataset for LTR retrotransposons. Almost two-thirds (37) of the 59 families identified consist of copia-like elements, but gypsy-like elements outnumber copia-like elements by a ratio of approximately 2:1. At least 17% of the rice genome consists of LTR retrotransposons. In addition to the ubiquitous gypsy- and copia-like classes of LTR retrotransposons, the rice genome contains at least two novel families of unusually small, non-coding (non-autonomous) LTR retrotransposons. CONCLUSIONS: Each of the major clades of rice LTR retrotransposons is more closely related to elements present in other species than to the other clades of rice elements, suggesting that horizontal transfer may have occurred over the evolutionary history of rice LTR retrotransposons. Like LTR retrotransposons in other species with relatively small genomes, many rice LTR retrotransposons are relatively young, indicating a high rate of turnover

Evolutionary history of Oryza sativa LTR retrotransposons: a preliminary survey of the rice genome sequences

BACKGROUND: LTR Retrotransposons transpose through reverse transcription of an RNA intermediate and are ubiquitous components of all eukaryotic genomes thus far examined. Plant genomes, in particular, have been found to be comprised of a remarkably high number of LTR retrotransposons. There is a significant body of direct and indirect evidence that LTR retrotransposons have contributed to gene and genome evolution in plants. RESULTS: To explore the evolutionary history of long terminal repeat (LTR) retrotransposons and their impact on the genome of Oryza sativa, we have extended an earlier computer-based survey to include all identifiable full-length, fragmented and solo LTR elements in the rice genome database as of April 2002. A total of 1,219 retroelement sequences were identified, including 217 full-length elements, 822 fragmented elements, and 180 solo LTRs. In order to gain insight into the chromosomal distribution of LTR-retrotransposons in the rice genome, a detailed examination of LTR-retrotransposon sequences on Chromosome 10 was carried out. An average of 22.3 LTR-retrotransposons per Mb were detected in Chromosome 10. CONCLUSIONS: Gypsy-like elements were found to be >4 × more abundant than copia-like elements. Eleven of the thirty-eight investigated LTR-retrotransposon families displayed significant subfamily structure. We estimate that at least 46.5% of LTR-retrotransposons in the rice genome are older than the age of the species (< 680,000 years). LTR-retrotransposons present in the rice genome range in age from those just recently inserted up to nearly 10 million years old. Approximately 20% of LTR retrotransposon sequences lie within putative genes. The distribution of elements across chromosome 10 is non-random with the highest density (48 elements per Mb) being present in the pericentric region

Thermodynamics of concentrated solid solution alloys

This paper reviews the three main approaches for predicting the formation of concentrated solid solution alloys (CSSA) and for modeling their thermodynamic properties, in particular, utilizing the methodologies of empirical thermo-physical parameters, CALPHAD method, and first-principles calculations combined with hybrid Monte Carlo/Molecular Dynamics (MC/MD) simulations. In order to speed up CSSA development, a variety of empirical parameters based on Hume-Rothery rules have been developed. Herein, these parameters have been systematically and critically evaluated for their efficiency in predicting solid solution formation. The phase stability of representative CSSA systems is then illustrated from the perspectives of phase diagrams and nucleation driving force plots of the σ phase using CALPHAD method. The temperature-dependent total entropies of the FCC, BCC, HCP, and σ phases in equimolar compositions of various systems are presented next, followed by the thermodynamic properties of mixing of the BCC phase in Al-containing and Ti-containing refractory metal systems. First-principles calculations on model FCC, BCC and HCP CSSA reveal the presence of both positive and negative vibrational entropies of mixing, while the calculated electronic entropies of mixing are negligible. Temperature dependent configurational entropy is determined from the atomic structures obtained from MC/MD simulations. Current status and challenges in using these methodologies as they pertain to thermodynamic property analysis and CSSA design are discussed

YAP and TAZ are transcriptional co-activators of AP-1 proteins and STAT3 during breast cellular transformation

The YAP and TAZ paralogs are transcriptional co-activators recruited to target sites by TEAD proteins. Here, we show that YAP and TAZ are also recruited by JUNB (a member of the AP-1 family) and STAT3, key transcription factors that mediate an epigenetic switch linking inflammation to cellular transformation. YAP and TAZ directly interact with JUNB and STAT3 via a WW domain important for transformation, and they stimulate transcriptional activation by AP-1 proteins. JUNB, STAT3, and TEAD co-localize at virtually all YAP/TAZ target sites, yet many target sites only contain individual AP-1, TEAD, or STAT3 motifs. This observation and differences in relative crosslinking efficiencies of JUNB, TEAD, and STAT3 at YAP/TAZ target sites suggest that YAP/TAZ is recruited by different forms of an AP-1/STAT3/TEAD complex depending on the recruiting motif. The different classes of YAP/TAZ target sites are associated with largely non-overlapping genes with distinct functions. A small minority of target sites are YAP- or TAZ-specific, and they are associated with different sequence motifs and gene classes from shared YAP/TAZ target sites. Genes containing either the AP-1 or TEAD class of YAP/TAZ sites are associated with poor survival of breast cancer patients with the triple-negative form of the disease

YAP and TAZ are transcriptional co-activators of AP-1 proteins and STAT3 during breast cellular transformation [preprint]

The YAP and TAZ paralogues are transcriptional co-activators recruited to target sites, primarily by TEAD proteins. Here, we show that YAP and TAZ are also recruited by JUNB and STAT3, key factors that mediate an epigenetic switch linking inflammation to cellular transformation. YAP and TAZ directly interact with JUNB and STAT3 via a WW domain important for transformation, co-occupy many target sites in vivo via AP-1 and (to a lesser extent) STAT3 sequence motifs, and stimulate transcriptional activation by AP-1 proteins. A few target sites are YAP- or TAZ-specific, and they are associated with different sequence motifs and gene classes. YAP/TAZ, JUNB, and STAT3 directly regulate a common set of target genes that overlap, but are distinct from, those regulated by YAP/TAZ and TEADs. The set of genes regulated by YAP/TAZ, STAT3, and JUNB is associated with poor survival in breast cancer patients with the triple-negative form of the disease