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Noble, D. (2013). Physiology is rocking the foundations of evolutionary biology. Exp Physiol, .
Abstract: The 'Modern Synthesis' (Neo-Darwinism) is a mid-twentieth century gene-centric view of evolution, based on random mutations accumulating to produce gradual change through natural selection. Any role of physiological function in influencing genetic inheritance was excluded. The organism became a mere carrier of the real objects of selection: its genes. We now know that genetic change is far from random and often not gradual. Molecular genetics and genome sequencing have deconstructed this unnecessarily restrictive view of evolution in a way that reintroduces physiological function and interactions with the environment as factors influencing the speed and nature of inherited change. Acquired characteristics can be inherited, and in a few but growing number of cases that inheritance has now been shown to be robust for many generations. The twenty-first century can look forward to a new synthesis that will reintegrate physiology with evolutionary biology.
Keywords: Gene expression; epigenetics; evolutionary biology; modern synthesis
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Castleberry, S., Wang, M., & Hammond, P. T. (2013). Nanolayered siRNA Dressing for Sustained Localized Knockdown. ACS Nano, .
Abstract: The success of RNA interference (RNAi) in medicine relies on the development of technology capable of successfully delivering it to tissues of interest. Significant research has focused on the difficult task of systemic delivery of RNAi; however its local delivery could be a more easily realized approach. Localized delivery is of particular interest for many medical applications, including the treatment of localized diseases, the modulation of cellular response to implants or tissue engineering constructs, and the management of wound healing and regenerative medicine. In this work we present an ultrathin electrostatically assembled coating for localized and sustained delivery of short interfering RNA (siRNA). This film was applied to a commercially available woven nylon dressing commonly used for surgical applications and was demonstrated to sustain significant knockdown of protein expression in multiple cell types for more than one week in vitro. Significantly, this coating can be easily applied to a medically relevant device and requires no externally delivered transfection agents for effective delivery of siRNA. These results present promising opportunities for the localized administration of RNAi.
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Poloni, A., Goteri, G., Zizzi, A., Serrani, F., Trappolini, S., Costantini, B., et al. (2013). Prognostic role of immunohistochemical analysis of 5mc in Myelodysplastic Syndromes. Eur J Haematol, .
Abstract: BACKGROUND: Aberrant DNA methylation at CpG islands within promoters is increasingly recognised as a common event in human cancers and has been associated with the silencing of important tumour suppressor genes. Epigenetic therapy using hypomethylating agents has demonstrated clinical effectiveness; the drugs azacitidine and decitabine have been approved for the treatment of MDS. METHOD: We investigated the association between global DNA methylation and clinical outcome in MDS. We evaluated 134 MDS bone marrow trephine biopsies (BMTB) by immunohistochemistry and compared the results with those from an age-matched group of normal BMTB. Immunohistochemistry was performed on paraffin-embedded sections using the anti-5-methylcytosine (5mc) antibody. RESULTS: Our results showed that the 5mc immunostaining score (M-score) of MDS patients was higher than those of normal controls and that overall survival significantly correlated with global DNA methylation, age, and IPSS score. Therefore, we found that patients with high levels of methylation had a shorter median overall survival (OS) compared to patients with lower levels. These immunohistochemistry results were confirmed by analysing global DNA methylation on LINE-1 sequences using the COBRA method and pyrosequencing. CONCLUSION: This study reports that global DNA methylation detected by immunohistochemistry predicts OS in MDS. This article is protected by copyright. All rights reserved.
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Swalm, B. M., Hallenbeck, K. K., Majer, C. R., Jin, L., Scott, M. P., Moyer, M. P., et al. (2013). Convergent Evolution of Chromatin Modification by Structurally Distinct Enzymes: Comparative Enzymology of Histone 3 Lysine 27 Methylation by Human Polycomb Repressive Complex 2 and Viral vSET. Biochem J, .
Abstract: Histone H3 lysine 27 (H3K27) methylation is an important epigenetic modification that regulates gene transcription. In humans, EZH1 and EZH2 are the only enzymes capable of catalyzing methylation of H3K27. There is great interest in understanding structure-function relationships for EZH2, as genetic alterations in this enzyme are thought to play a causal role in a number of human cancers. EZH2 is challenging to study because it is only active in the context of the multi-subunit Polycomb Repressive Complex 2 (PRC2). vSET is a viral lysine methyltransferase that represents the smallest protein unit capable of catalyzing H3K27 methylation. The crystal structure of this minimal catalytic protein has been solved and researchers have suggested that vSET might prove useful as an EZH2 surrogate for the development of active site-directed inhibitors. To test this proposition, we conducted comparative enzymatic analysis of human EZH2 and vSET and report that while both enzymes share similar preferences for methylation of H3K27, they diverge in terms of their permissiveness for catalyzing methylation of alternative histone lysine sites, their relative preferences for utilization of multimeric, macromolecular substrates, their active site primary sequences and most important, their sensitivity to inhibition by drug-like small molecules. The cumulative data lead us to suggest that EZH2 and vSET have very distinct active site structures, despite the commonality of the reaction catalyzed by the two enzymes. Hence, the EZH2 and vSET pair of enzymes represent an example of convergent evolution in which distinct structural solutions have developed to solve a common catalytic need.
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Kiran, S., Chatterjee, N. M., Singh, S., Kaul, S. C., Wadhwa, R., & Ramakrishna, G. (2013). Intracellular distribution of human SIRT7 and mapping of the nucle(ol)ar localization signal. Febs J, .
Abstract: Sirtuins belong to a class of NAD-dependent deacetylases and consists of seven distinct isoforms of which SIRT7 is the least studied member. In the present study, the subcellular expression of SIRT7 in primary fibroblasts undergoing senescence was evaluated by immunocytochemistry and immunoblot assay. Expression of nucleolar SIRT7 in young fibroblast was very prominent, decreased during late passages and became undetectable in the senescent cells. Interestingly, we found hitherto unknown staining for cytoplasmic SIRT7 in fibroblasts. We now report existence of steady state level of SIRT7 in cytoplasm. Selective localization of the high molecular weight (47.5-kDa) SIRT7 in the cytoplasmic fraction and the low molecular weight (45-kDa) in the nuclear fraction was observed in the immunoblot analysis from various cell types. Specificity of the N-terminal antibodies to detect the cytoplasmic SIRT7 was confirmed by RNAi and peptide competition assays. The two forms of SIRT7 toggled in expression following serum starvation, nocodazole and okadaic acid treatments and also during senescence. Using a combination of deletion constructs and site directed mutagenesis we now define the role of two distinct SIRT7 sequences in N-terminal (61-76 aa, LQGRSRRREGLKRRQE) and C-terminal (392-400 aa, KRTKRKKVT) regions for nuclear and nucleolar import, respectively. In conclusion, we report for the first time the existence of a cytoplasmic pool of SIRT7 besides its well known nucleolar entity; and distinct localization signals for its nucle(ol)ar targeting, and an association between loss of nucleolar SIRT7 and replicative senescence. This article is protected by copyright. All rights reserved.
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