Towards an Evolutionary Model of Transcription Networks

DNA evolution models made invaluable contributions to comparative genomics, although it seemed formidable to include non-genomic features into these models. In order to build an evolutionary model of transcription networks (TNs), we had to forfeit the substitution model used in DNA evolution and to start from modeling the evolution of the regulatory relationships. We present a quantitative evolutionary model of TNs, subjecting the phylogenetic distance and the evolutionary changes of cis-regulatory sequence, gene expression and network structure to one probabilistic framework. Using the genome sequences and gene expression data from multiple species, this model can predict regulatory relationships between a transcription factor (TF) and its target genes in all species, and thus identify TN re-wiring events. Applying this model to analyze the pre-implantation development of three mammalian species, we identified the conserved and re-wired components of the TNs downstream to a set of TFs including Oct4, Gata3/4/6, cMyc and nMyc. Evolutionary events on the DNA sequence that led to turnover of TF binding sites were identified, including a birth of an Oct4 binding site by a 2nt deletion. In contrast to recent reports of large interspecies differences of TF binding sites and gene expression patterns, the interspecies difference in TF-target relationship is much smaller. The data showed increasing conservation levels from genomic sequences to TF-DNA interaction, gene expression, TN, and finally to morphology, suggesting that evolutionary changes are larger at molecular levels and smaller at functional levels. The data also showed that evolutionarily older TFs are more likely to have conserved target genes, whereas younger TFs tend to have larger re-wiring rates

Sharing vocabularies: towards horizontal alignment of values-driven business functions

This paper highlights the emergence of different ‘vocabularies’ that describe various values-driven business functions within large organisations and argues for improved horizontal alignment between them. We investigate two established functions that have long-standing organisational histories: Ethics and Compliance (E&C) and Corporate Social Responsibility (CSR). By drawing upon research on organisational alignment, we explain both the need for and the potential benefit of greater alignment between these values-driven functions. We then examine the structural and socio-cultural dimensions of organisational systems through which E&C and CSR horizontal alignment can be coordinated to improve synergies, address tensions, and generate insight to inform future research and practice in the field of Business and Society. The paper concludes with research questions that can inform future scholarly research and a practical model to guide organizations’ efforts towards inter-functional, horizontal alignment of values-driven organizational practice

Pleiotropic effect of the proton pump inhibitor esomeprazole leading to suppression of lung inflammation and fibrosis

Background: The beneficial outcome associated with the use of proton pump inhibitors (PPIs) in idiopathic pulmonary fibrosis (IPF) has been reported in retrospective studies. To date, no prospective study has been conducted to confirm these outcomes. In addition, the potential mechanism by which PPIs improve measures of lung function and/or transplant-free survival in IPF has not been elucidated. Methods: Here, we used biochemical, cell biological and preclinical studies to evaluate regulation of markers associated with inflammation and fibrosis. In our in vitro studies, we exposed primary lung fibroblasts, epithelial and endothelial cells to ionizing radiation or bleomycin; stimuli typically used to induce inflammation and fibrosis. In addition, we cultured lung fibroblasts from IPF patients and studied the effect of esomeprazole on collagen release. Our preclinical study tested efficacy of esomeprazole in a rat model of bleomycin-induced lung injury. Furthermore, we performed retrospective analysis of interstitial lung disease (ILD) databases to examine the effect of PPIs on transplant-free survival. Results: The cell culture studies revealed that esomeprazole controls inflammation by suppressing the expression of pro-inflammatory molecules including vascular cell adhesion molecule-1, inducible nitric oxide synthase, tumor necrosis factor-alpha (TNF-alpha) and interleukins (IL-1 beta and IL-6). The antioxidant effect is associated with strong induction of the stress-inducible cytoprotective protein heme oxygenase-1 (HO1) and the antifibrotic effect is associated with potent inhibition of fibroblast proliferation as well as downregulation of profibrotic proteins including receptors for transforming growth factor beta (TGF beta), fibronectin and matrix metalloproteinases (MMPs). Furthermore, esomeprazole showed robust effect in mitigating the inflammatory and fibrotic responses in a murine model of acute lung injury. Finally, retrospective analysis of two ILD databases was performed to assess the effect of PPIs on transplant-free survival in IPF patients. Intriguingly, this data demonstrated that IPF patients on PPIs had prolonged survival over controls (median survival of 3.4 vs 2 years). Conclusions: Overall, these data indicate the possibility that PPIs may have protective function in IPF by directly modulating the disease process and suggest that they may have other clinical utility in the treatment of extra-intestinal diseases characterized by inflammatory and/or fibrotic phases.Stanford School of Medicine [1049528-149- KAVFB]; Tobacco-Related Disease Research Program of the University of California [20FT-0090]; National Institutes of Health National Heart, Lung, and Blood Institute [5K01HL118683, P01HL114470]; Houston Methodist Research Institute [25150001]; Stanford SPARK Translational Research ProgramSCI(E)[email protected]

Mandibular reconstruction and osseointegrated implants after tumour reconstruction

Acoustoelastic stress measurement has been established for bulk shear wave, in particular with birefringence of the wave. This method, however, evaluates only average stress over thickness of a sample. Some preliminary studies have been reported for local surface stress measurement with Rayleigh or leaky Rayleigh wave. An approach using an acoustic microscope operated with burst waves over 100MHz [1, 2] is markedly sensitive to surface roughness and anisotropy of grains due to very short wave length of the wave. The other approach using contact transducers needs long propagation distance [3, 4]

Expression of BMP-2 and TGF-?1 mRNA during healing of the rabbit mandible

To identify the cell types which produce BMP and TGF-β during fracture healing and to elucidate the interactions between BMP and TGF-β in regulating cell proliferation and differentiation at various stages, an experimental model of fracture healing in the rabbit mandible was established and the expression of BMP-2 and TGF-β1 mRNA was studied at different healing stages by in situ hybridization. The results showed that undifferentiated mesenchymal cells, differentiating osteoblasts and chondroblasts, had higher levels of BMP-2 mRNA at the stage of intramembranous bone formation and early chondrogenesis, while the level of TGF-β1 mRNA was higher in chondrocytes and active differentiated osteoblasts during chondrogenesis and endochondral ossification, respectively. We conclude that BMP-2 expression was correlated with the differentiation of mesenchymal cells into osteoblasts and chondrocytes. TGF-β1 mRNA expression was closely associated with the active synthetic stage of osteoblasts and chondrocytes. These observations suggest that both BMP and TGF-β are involved in the regulation of fracture healing. BMP may play an important rôle in bone induction and early chondrogenesis, while TGF-β regulates the proliferation and active synthetic ability of chondrocytes and osteoblasts. © Munksgaard, 1997.link_to_subscribed_fulltex

From Developmental Constraint to Evolvability How Concepts Figure in Explanation and Disciplinary Identity

Abstract The concept of developmental constraint was at the heart of developmental approaches to evolution of the 1980s. While this idea was widely used to criticize neo-Darwinian evolutionary theory, critique does not yield an alternative framework that offers evolutionary explanations. In current Evo-devo the concept of constraint is of minor importance, whereas notions as evolvability are at the center of attention. The latter clearly defines an explanatory agenda for evolutionary research, so that one could view the historical shift from ‘developmental constraint’ towards ‘evolvability ’ as the move from a concept that is a mere tool of criticism to a concept that establishes a positive explanatory project. However, by taking a look at how the concept of constraint was employed in the 1980s, I argue that developmental constraint was not just seen as restricting possibilities (‘constraining’), but also as facilitating morphological change in several ways. Accounting for macroevolutionary transformation and the origin of novel form was an aim of these developmental approaches to evolution. Thus, the concept of developmental constraint was part of a positive explanatory agenda long before th