Search for cosmological mu variation from high redshift H2 absorption; a status report

Observations of H2 spectra in the line-of-sight of distant quasars may reveal a variation of the proton-electron mass ratio mu=m_p/m_e at high redshift, typically for z>2. Currently four high-quality systems (Q0347-383, Q0405-443, Q0528-250 and J2123-005) have been analyzed returning a constraint Dmu/mu < 1 x 10^{-5}. We present data and a mu-variation analysis of another system, Q2348-011 at redshift z_{abs}=2.42, delivering dmu/mu = (-1.5 \pm 1.6) x 10^{-5}. In addition to observational data the status of the laboratory measurements is reviewed. The future possibilities of deriving a competitive constraint on Dmu/mu from the known high-redshift H2 absorbers is investigated, resulting in the identification of a number of potentially useful systems for detecting mu-variation.Comment: 13 Pages, 4 Figures, JENAM conference (Lisbon); accepte

RAD21 Cooperates with Pluripotency Transcription Factors in the Maintenance of Embryonic Stem Cell Identity

For self-renewal, embryonic stem cells (ESCs) require the expression of specific transcription factors accompanied by a particular chromosome organization to maintain a balance between pluripotency and the capacity for rapid differentiation. However, how transcriptional regulation is linked to chromosome organization in ESCs is not well understood. Here we show that the cohesin component RAD21 exhibits a functional role in maintaining ESC identity through association with the pluripotency transcriptional network. ChIP-seq analyses of RAD21 reveal an ESC specific cohesin binding pattern that is characterized by CTCF independent co-localization of cohesin with pluripotency related transcription factors Oct4, Nanog, Sox2, Esrrb and Klf4. Upon ESC differentiation, most of these binding sites disappear and instead new CTCF independent RAD21 binding sites emerge, which are enriched for binding sites of transcription factors implicated in early differentiation. Furthermore, knock-down of RAD21 causes expression changes that are similar to expression changes after Nanog depletion, demonstrating the functional relevance of the RAD21 - pluripotency transcriptional network association. Finally, we show that Nanog physically interacts with the cohesin or cohesin interacting proteins STAG1 and WAPL further substantiating this association. Based on these findings we propose that a dynamic placement of cohesin by pluripotency transcription factors contributes to a chromosome organization supporting the ESC expression program

5C analysis of the Epidermal Differentiation Complex locus reveals distinct chromatin interaction networks between gene-rich and gene-poor TADs in skin epithelial cells

YesMammalian genomes contain several dozens of large (>0.5 Mbp) lineage-specific gene loci harbouring functionally related genes. However, spatial chromatin folding, organization of the enhancer-promoter networks and their relevance to Topologically Associating Domains (TADs) in these loci remain poorly understood. TADs are principle units of the genome folding and represents the DNA regions within which DNA interacts more frequently and less frequently across the TAD boundary. Here, we used Chromatin Conformation Capture Carbon Copy (5C) technology to characterize spatial chromatin interaction network in the 3.1 Mb Epidermal Differentiation Complex (EDC) locus harbouring 61 functionally related genes that show lineage-specific activation during terminal keratinocyte differentiation in the epidermis. 5C data validated by 3D-FISH demonstrate that the EDC locus is organized into several TADs showing distinct lineage-specific chromatin interaction networks based on their transcription activity and the gene-rich or gene-poor status. Correlation of the 5C results with genome-wide studies for enhancer-specific histone modifications (H3K4me1 and H3K27ac) revealed that the majority of spatial chromatin interactions that involves the gene-rich TADs at the EDC locus in keratinocytes include both intra- and inter-TAD interaction networks, connecting gene promoters and enhancers. Compared to thymocytes in which the EDC locus is mostly transcriptionally inactive, these interactions were found to be keratinocyte-specific. In keratinocytes, the promoter-enhancer anchoring regions in the gene-rich transcriptionally active TADs are enriched for the binding of chromatin architectural proteins CTCF, Rad21 and chromatin remodeler Brg1. In contrast to gene-rich TADs, gene-poor TADs show preferential spatial contacts with each other, do not contain active enhancers and show decreased binding of CTCF, Rad21 and Brg1 in keratinocytes. Thus, spatial interactions between gene promoters and enhancers at the multi-TAD EDC locus in skin epithelial cells are cell type-specific and involve extensive contacts within TADs as well as between different gene-rich TADs, forming the framework for lineage-specific transcription.This study was supported by the grants 5R01AR064580 and 1RO1AR071727 to VAB, TKS and AAS, as well as by the grants from MRC (MR/ M010015/1) and BBSRC (BB/K010050/1) to VAB

Enhancing Biological and Biomechanical Fixation of Osteochondral Scaffold: A Grand Challenge

Osteoarthritis (OA) is a degenerative joint disease, typified by degradation of cartilage and changes in the subchondral bone, resulting in pain, stiffness and reduced mobility. Current surgical treatments often fail to regenerate hyaline cartilage and result in the formation of fibrocartilage. Tissue engineering approaches have emerged for the repair of cartilage defects and damages to the subchondral bones in the early stage of OA and have shown potential in restoring the joint's function. In this approach, the use of three-dimensional scaffolds (with or without cells) provides support for tissue growth. Commercially available osteochondral (OC) scaffolds have been studied in OA patients for repair and regeneration of OC defects. However, some controversial results are often reported from both clinical trials and animal studies. The objective of this chapter is to report the scaffolds clinical requirements and performance of the currently available OC scaffolds that have been investigated both in animal studies and in clinical trials. The findings have demonstrated the importance of biological and biomechanical fixation of the OC scaffolds in achieving good cartilage fill and improved hyaline cartilage formation. It is concluded that improving cartilage fill, enhancing its integration with host tissues and achieving a strong and stable subchondral bone support for overlying cartilage are still grand challenges for the early treatment of OA

Outcomes of Extensive Hybridization and Introgression in Epidendrum (Orchidaceae): Can We Rely on Species Boundaries?

Hybridization has the potential to contribute to phenotypic and genetic variation and can be a major evolutionary mechanism. However, when hybridization is extensive it can also lead to the blurring of species boundaries and the emergence of cryptic species (i.e., two or more species not distinguishable morphologically). In this study, we address this hypothesis in Epidendrum, the largest Neotropical genus of orchids where hybridization is apparently so common that it may explain the high levels of morphological diversity found. Nonetheless, this hypothesis is mostly based on the intermediacy of morphological characters and intermediacy by itself is not a proof of hybridization. Therefore, in this study, we first assessed the existence of hybrids using cpDNA and AFLP data gathered from a large-scale sampling comprising 1038 plants of three species of Epidendrum (E. calanthum, E. cochlidium and E. schistochilum). Subsequently, a Bayesian assignment of individuals into different genetic classes (pure species, F1, F2 or backcross generations) revealed that hybrid genotypes were prevalent in all sympatric populations. In most cases, parental species were not assigned as pure individuals, rather consisting in backcrossed genotypes or F1 hybrids. We also found that reproductive barriers are apparently very weak in Epidendrum because the three species largely overlapped in their flowering periods and interspecific crosses always produced viable seeds. Further, hybridization contributed to enhance floral variability, genome size and reproductive success since we found that these traits were always higher in hybrid classes (F1, F2 and backcrosses) than in pure parental species, and offer an explanation for the blurring of species boundaries in this genus of orchids. We hypothesize that these natural hybrids possess an evolutionary advantage, which may explain the high rates of cryptic species observed in this genus.UTPL financed the work of IM though a postdoctoral grant (PROY-CBCM-0021) and the Portuguese Foundation for Science and Technology and European Social Funds financed the work of SC (FCT/SFRH/BPD/41200/2007)