Structure and decay of a proto-Y region in Tilapia, Oreochromis niloticus

Funding for Open Access provided by the UMD Libraries Open Access Publishing Fund.Sex-determination genes drive the evolution of adjacent chromosomal regions. Sexually antagonistic selection favors the accumulation of inversions that reduce recombination in regions adjacent to the sex-determination gene. Once established, the clonal inheritance of sex-linked inversions leads to the accumulation of deleterious alleles, repetitive elements and a gradual decay of sex-linked genes. This in turn creates selective pressures for the evolution of mechanisms that compensate for the unequal dosage of gene expression. Here we use whole genome sequencing to characterize the structure of a young sex chromosome and quantify sex-specific gene expression in the developing gonad. We found an 8.8 Mb block of strong differentiation between males and females that corresponds to the location of a previously mapped sex-determiner on linkage group 1 of Oreochromis niloticus. Putatively disruptive mutations are found in many of the genes within this region. We also found a significant female-bias in the expression of genes within the block of differentiation compared to those outside the block of differentiation. Eight candidate sex-determination genes were identified within this region. This study demonstrates a block of differentiation on linkage group 1, suggestive of an 8.8 Mb inversion encompassing the sex-determining locus. The enrichment of female-biased gene expression inside the proposed inversion suggests incomplete dosage compensation. This study helps establish a model for studying the early-to-intermediate stages of sex chromosome evolution.https://doi.org/10.1186/1471-2164-15-97

Photochemistry of framework-supported M(diimine)(CO)₃X complexes in 3D Lithium-Carboxylate metal−organic frameworks: monitoring the effect of framework cations

The structures and photochemical behaviour of two new metal-organic frameworks are reported. Reaction of Re(2,2ʹ-bipyʹ-5,5ʹ-dicarboxylic acid)(CO)₃Cl or Mn(2,2ʹ-bipyʹ-5,5ʹ- dicarboxylic acid)(CO)₃Br with either LiCl or LiBr, respectively, produces single crystals of {Li₂(DMF)₂[(2,2ʹ-bipyʹ-5,5ʹ-dicarboxylate)Re(CO)₃Cl]}n (ReLi) or {Li₂(DMF)₂[(2,2ʹ-bipyʹ- 5,5ʹ-dicarboxylate)Mn(CO)₃Br]}n (MnLi). The structures formed by the two MOFs comprise one-dimensional chains of carboxylate-bridged Li(I) cations that are cross-linked by units of Re(2,2ʹ-bipyʹ-5,5ʹ-dicarboxylate)(CO)₃Cl (ReLi) or Mn(2,2ʹ-bipyʹ-5,5ʹ- dicarboxylate)(CO)₃Br (MnLi). The photophysical and photochemical behaviour of both ReLi and MnLi are probed. The rhenium-containing MOF, ReLi, exhibits luminescence and the excited state behaviour, as established by time-resolved infra-red measurements, are closer in behaviour to that of unsubstituted [Re(bipy)(CO)₃Cl] rather than a related MOF where the Li(I) cations are replaced by Mn(II) cations. These observations are further supported by DFT calculations. Upon excitation MnLi forms a dicarbonyl species which rapidly recombines with the dissociated CO, in a fashion consistent with the majority of the photoejected CO not escaping the MOF channels

Polarization and Belief Dynamics in the Black and White Communities: An Agent-Based Network Model from the Data

Public health care interventions—regarding vaccination, obesity, and HIV, for example—standardly take the form of information dissemination across a community. But information networks can vary importantly between different ethnic communities, as can levels of trust in information from different sources. We use data from the Greater Pittsburgh Random Household Health Survey to construct models of information networks for White and Black communities--models which reflect the degree of information contact between individuals, with degrees of trust in information from various sources correlated with positions in that social network. With simple assumptions regarding belief change and social reinforcement, we use those modeled networks to build dynamic agent-based models of how information can be expected to flow and how beliefs can be expected to change across each community. With contrasting information from governmental and religious sources, the results show importantly different dynamic patterns of belief polarization within the two communities

Transcriptional recapitulation and subversion of embryonic colon development by mouse colon tumor models and human colon cancer

Colon tumors from four independent mouse models and 100 human colorectal cancers all exhibited striking recapitulation of embryonic colon gene expression from embryonic days 13.5-18.5

Transcriptional recapitulation and subversion of embryonic colon development by mouse colon tumor models and human colon cancer

Abstract Background The expression of carcino-embryonic antigen by colorectal cancer is an example of oncogenic activation of embryonic gene expression. Hypothesizing that oncogenesis-recapitulating-ontogenesis may represent a broad programmatic commitment, we compared gene expression patterns of human colorectal cancers (CRCs) and mouse colon tumor models to those of mouse colon development embryonic days 13.5-18.5. Results We report here that 39 colon tumors from four independent mouse models and 100 human CRCs encompassing all clinical stages shared a striking recapitulation of embryonic colon gene expression. Compared to normal adult colon, all mouse and human tumors over-expressed a large cluster of genes highly enriched for functional association to the control of cell cycle progression, proliferation, and migration, including those encoding MYC, AKT2, PLK1 and SPARC. Mouse tumors positive for nuclear β-catenin shifted the shared embryonic pattern to that of early development. Human and mouse tumors differed from normal embryonic colon by their loss of expression modules enriched for tumor suppressors (EDNRB, HSPE, KIT and LSP1). Human CRC adenocarcinomas lost an additional suppressor module (IGFBP4, MAP4K1, PDGFRA, STAB1 and WNT4). Many human tumor samples also gained expression of a coordinately regulated module associated with advanced malignancy (ABCC1, FOXO3A, LIF, PIK3R1, PRNP, TNC, TIMP3 and VEGF). Conclusion Cross-species, developmental, and multi-model gene expression patterning comparisons provide an integrated and versatile framework for definition of transcriptional programs associated with oncogenesis. This approach also provides a general method for identifying pattern-specific biomarkers and therapeutic targets. This delineation and categorization of developmental and non-developmental activator and suppressor gene modules can thus facilitate the formulation of sophisticated hypotheses to evaluate potential synergistic effects of targeting within- and between-modules for next-generation combinatorial therapeutics and improved mouse models

Consensus guidelines for the use and interpretation of angiogenesis assays

The formation of new blood vessels, or angiogenesis, is a complex process that plays important roles in growth and development, tissue and organ regeneration, as well as numerous pathological conditions. Angiogenesis undergoes multiple discrete steps that can be individually evaluated and quantified by a large number of bioassays. These independent assessments hold advantages but also have limitations. This article describes in vivo, ex vivo, and in vitro bioassays that are available for the evaluation of angiogenesis and highlights critical aspects that are relevant for their execution and proper interpretation. As such, this collaborative work is the first edition of consensus guidelines on angiogenesis bioassays to serve for current and future reference