Nuclear translocation of cytochrome c during apoptosis

Release of cytochrome c from mitochondria is a major event during apoptosis. Released cytochrome c has been shown to activate caspase-dependent apoptotic signals. In this report, we provide evidence for a novel role of cytochrome c in caspase-independent nuclear apoptosis. We showed that cytochrome c, released from mitochondria upon apoptosis induction, gradually accumulates in the nucleus as evidenced by both immunofluorescence and subcellular fractionation. Parallel to nuclear accumulation of cytochrome c, acetylated histone H2A, but not unmodified H2A, was released from the nucleus to the cytoplasm. Addition of purified cytochrome c to isolated nuclei recapitulated the preferential release of acetylated, but not deacetylated, histone H2A. Cytochrome c was also found to induce chromatin condensation. These results suggest that the nuclear accumulation of cytochrome c may be directly involved in the remodeling of chromatin. Our results provide evidence of a novel role for cytochrome c in inducing nuclear apoptosis.

Fatty acid derivatised analogues of glucose-dependent insulinotropic polypeptide with improved antihyperglycaemic and insulinotropic properties

C-terminal acylation of Lys(37) with myristic (MYR; tetradecanoic acid), palmitic (PAL; hexadecanoic acid) and stearic (octadecanoic acid) fatty acids with or without N-terminal acetylation was employed to develop long-acting analogues of the glucoregulatory hormone, glucose-dependent insulinotropic polypeptide (GIP). All GIP analogues exhibited resistance to dipeptidylpeptidase-IV (DPP-IV) and significantly improved in vitro cAMP production and insulin secretion. Administration of GIP analogues to ob/ob mice significantly lowered plasma glucose-GIP(Lys(37)MYR), N-AcGIP(Lys(37)MYR) and GIP(Lys(37)PAL) increased plasma insulin concentrations. GIP(Lys(37)MYR) and N-AcGIP(Lys(37)MYR) elicited protracted glucose-lowering effects when administered 24h prior to an intraperitoneal glucose load. Daily administration of GIP(Lys(37)MYR) and N-AcGIP(Lys(37)MYR) to ob/ob mice for 24 days decreased glucose and significantly improved plasma insulin, glucose tolerance and beta-cell glucose responsiveness. Insulin sensitivity, pancreatic insulin content and triglyceride levels were not changed. These data demonstrate that C-terminal acylation particularly with myristic acid provides a class of stable, longer-acting forms of GIP for further evaluation in diabetes therapy.

Hydroxyl functionalities of middle rank british coals

Most of the new processes involving the utilisation of coal are based on hydroliquefaction, and in order to assess the suitability of the various coals for this purpose and to characterise coals in general, it is desirable to have a detailed and accurate knowledge of their chemical constitution and reactivity. Also, in the consumption of coals as chemical feed stocks, as in hydroliquefaction, it is advantageous to classify the coals in terms of chemical parameters as opposed to, or in addition to, carbonisation parameters. In view of this it is important to realise the functional groups on the coal hydrocarbon skeleton. In this research it was attempted to characterise coals of various rank (and subsequently their macerals) via methods involving both microwave-driven and bench top derivatisation of the hydroxyl functionalities present in coal. These hydroxyl groups are predominantly in the form of hindered phenolic groups, with other alcoholic groupings being less important, in the coals studied here. Four different techniques were employed, three of which - stannylation, silylation and methylation - were based on in situ analysis. The fourth technique - acetylation - involved derivatisation followed by analysis of a leaving group. The four different techniques were critically compared and it is concluded that silylation is the most promising technique for the evaluation of the hydroxyl content of middle rank coals and coal macerals. Derivatisation via stannylation using TBTO was impeded due to the large steric demand of the reagent and acetylation did not successfully derivatise the more hindered phenolic groups. Three novel methylation techniques were investigated and two of these show great potential. The information obtained from the techniques was correlated together to give a comprehensive insight into the coals and coal macerals studied.

A spectroscope study of some semiquinone radical ions

The effect of substituents on the value of the oxidation potential of quinones is reviewed and attempts to prepare substituted diphenoquinones with high oxidation potentials are reported. Attempts to characterise the mechanism of addition and substitution in diphenoquinones by identifying the products of the Thiele acetylation of diphenoquinone are reported. The reaction proved most efficient when the incoming acetylinium ion is directed by substituents in the diphenoquinone. A 1,8-addition to diphenoquinone is reported and characterised by isolating the products of the reaction between acetyl chloride and diphenoquinone, with perchloric acid as catalyst. The alternating linewidth effects observed in e.s.r.spectra are discussed and applied to account for such effects observed in the e.s.r.spectra of diphenosemiquinone anion and cation radicals. The spectra are analysed and the intramolecular processes producing these effects are discussed. A dianion diradical where intramolecular rotation about the 1 - 1' bond is restricted is produced by the oxidation of 2,2' ,4,4' -tetra hydroxybiphenyl. Previous studies of diphenosemiquinone anions are reviewed and alkylated diphenosemiquinone anion are produced by the reduction of the parent quinone with potassium hydroxide solution, the resulting radical being stabilised by the presence of pyridine. A qualitative interpretation of the solvent-ion effect in alkylated diphenosemiquinone anions is given. Diphanosemiquinone cation radicals are reviewed and previous studies are re-examined.

Knowledge integration for analyzing ChIP-seq

To capture the genomic profiles for histone modification, chromatin immunoprecipitation (ChIP) is combined with next generation sequencing, which is called ChIP-seq. However, enriched regions generated from the ChIP-seq data are only evaluated on the limited knowledge acquired from manually examining the relevant biological literature. This paper proposes a novel framework, which integrates multiple knowledge sources such as biological literature, Gene Ontology, and microarray data. In order to precisely analyze ChIP-seq data for histone modification, knowledge integration is based on a unified probabilistic model. The model is employed to re-rank the enriched regions generated from peak finding algorithms. Through filtering the reranked enriched regions using some predefined threshold, more reliable and precise results could be generated. The combination of the multiple knowledge sources with the peaking finding algorithm produces a new paradigm for ChIP-seq data analysis. © (2012) Trans Tech Publications, Switzerland.

Post-translational modifications and mass spectrometry detection

In this review, we provide a comprehensive bibliographic overview of the role of mass spectrometry and the recent technical developments in the detection of post-translational modifications (PTMs). We briefly describe the principles of mass spectrometry for detecting PTMs and the protein and peptide enrichment strategies for PTM analysis, including phosphorylation, acetylation and oxidation. This review presents a bibliographic overview of the scientific achievements and the recent technical development in the detection of PTMs is provided. In order to ascertain the state of the art in mass spectrometry and proteomics methodologies for the study of PTMs, we analyzed all the PTM data introduced in the Universal Protein Resource (UniProt) and the literature published in the last three years. The evolution of curated data in UniProt for proteins annotated as being post-translationally modified is also analyzed. Additionally, we have undertaken a careful analysis of the research articles published in the years 2010 to 2012 reporting the detection of PTMs in biological samples by mass spectrometry. © 2013 Elsevier Inc.

Influence of Egr-1 in cardiac tissue-derived mesenchymal stem cells in response to glucose variations

Mesenchymal stem cells (MSCs) represent a promising cell population for cell therapy and regenerative medicine applications. However, how variations in glucose are perceived by MSC pool is still unclear. Since, glucose metabolism is cell type and tissue dependent, this must be considered when MSCs are derived from alternative sources such as the heart. The zinc finger transcription factor Egr-1 is an important early response gene, likely to play a key role in the glucose-induced response. Our aim was to investigate how short-term changes in in vitro glucose concentrations affect multipotent cardiac tissue-derived MSCs (cMSCs) in a mouse model of Egr-1 KO (Egr-1-/-). Results showed that loss of Egr-1 does not significantly influence cMSC proliferation. In contrast, responses to glucose variations were observed in wt but not in Egr-1 -/- cMSCs by clonogenic assay. Phenotype analysis by RT-PCR showed that cMSCs Egr-1-/- lost the ability to regulate the glucose transporters GLUT-1 and GLUT-4 and, as expected, the Egr-1 target genes VEGF, TGFβ-1, and p300. Acetylated protein levels of H3 histone were impaired in Egr-1-/- compared to wt cMSCs. We propose that Egr-1 acts as immediate glucose biological sensor in cMSCs after a short period of stimuli, likely inducing epigenetic modifications. © 2014 Daniela Bastianelli et al.

Efficient purification of chromatin architectural proteins:histones, HMGB proteins and FKBP3 (FKBP25) immunophilin

A two-step process of high ionic strength lysis of chicken erythrocyte cell nuclei followed by cation-exchange chromatography has separated at very high yield all the histone and HMGB (high-mobility group B) nuclear proteins, except the less-soluble histone tetramers. Surprisingly high yields of the nuclear immunophilin FKBP3 (FKBP25) and Hsp70 (heat-shock protein 70) co-fractionate with HMGB1 and HMGB3. Furthermore, these proteins can be separated by anion-exchange chromatography. The purified nuclear proteins retain their native, post-translational modification (PTM) marks, including those associated with chromatin-fibre remodelling. These marks are intimately associated with the control of the cell cycle. The methods herein are therefore of value for targeting these and other nuclear proteins for future proteomic studies in healthy and diseased cells. This journal is © 2012 The Royal Society of Chemistry.

A role for epigenetic modulation of the innate immune response during aging

The ageing process results from a complex interplay between genes and the environment that can precipitate an uncontrolled inflammation. Epigenetic changes are believed to provide a link between the environment and nutrition to gene expression by altering the activity of some histone-modifying protein. Epigenetic modifications of DNA and histone proteins have been proposed as important contributory mechanisms to the retention of metabolic memory over time. A thorough understanding of the posttranscriptional and epigenetic factors involved in both normal ageing and age-related disease may inform new strategies and approaches to diagnose, treat, or suppress many aspects of age-dependent frailty.

An investigation into the effects of metabolic disturbance on monocyte inflammatory response and regulation

The presence of chronic inflammation is associated with increased nutrient availability during obesity or type 2 diabetes which contributes to the development of complications such as atherosclerosis, stroke and myocardial infarction. The link between increased nutrient availability and inflammatory response remains poorly understood. The functioning of monocytes, the primary instigators of the inflammatory response was assessed in response to obesity and increased glucose availability. Monocyte microRNA expression was assessed in obese individuals prior to and up to one year after bariatric surgery. A number of microRNAs were identified to be dysregulated in obesity, some of which have previously been linked to the regulation of monocyte inflammatory responses including the microRNAs 146a-5p and 424-5p. Weight loss in response to bariatric surgery lead to the reversal of microRNA changes towards control values. In vitro treatments of THP-1 monocytes with high concentrations of D-glucose resulted in decreased intracellular NAD+:NADH ratio, decreased SIRT1 deacetylase activity and increased P65 acetylation. However the increased osmotic concentration inhibited LPS induced inflammatory response and TNFα mRNA expression. In vitro treatment of primary human monocytes with increased concentrations of D-glucose resulted in increased secretion of a number of inflammatory cytokines and increased expression of TNFα mRNA. Treatment also resulted in decreased intracellular NAD+:NADH ratio and increased binding of acetylated P65 to the TNFα promoter region. In vitro treatments of primary monocytes also replicated the altered expression of the microRNAs 146a-5p and miR-424-5p, as seen in obese individuals. In conclusion a number of changes in monocyte function were observed in response to obesity and treatment with high concentrations of D-glucose. These may lead to the dysregulation of inflammatory responses contributing to the development of co-morbidities.