Histone Variants and Their Post-Translational Modifications in Primary Human Fat Cells

Epigenetic changes related to human disease cannot be fully addressed by studies of cells from cultures or from other mammals. We isolated human fat cells from subcutaneous abdominal fat tissue of female subjects and extracted histones from either purified nuclei or intact cells. Direct acid extraction of whole adipocytes was more efficient, yielding about 100 µg of protein with histone content of 60% –70% from 10 mL of fat cells. Differential proteolysis of the protein extracts by trypsin or ArgC-protease followed by nanoLC/MS/MS with alternating CID/ETD peptide sequencing identified 19 histone variants. Four variants were found at the protein level for the first time; particularly HIST2H4B was identified besides the only H4 isoform earlier known to be expressed in humans. Three of the found H2A potentially organize small nucleosomes in transcriptionally active chromatin, while two H2AFY variants inactivate X chromosome in female cells. HIST1H2BA and three of the identified H1 variants had earlier been described only as oocyte or testis specific histones. H2AFX and H2AFY revealed differential and variable N-terminal processing. Out of 78 histone modifications by acetylation/trimethylation, methylation, dimethylation, phosphorylation and ubiquitination, identified from six subjects, 68 were found for the first time. Only 23 of these modifications were detected in two or more subjects, while all the others were individual specific. The direct acid extraction of adipocytes allows for personal epigenetic analyses of human fat tissue, for profiling of histone modifications related to obesity, diabetes and metabolic syndrome, as well as for selection of individual medical treatments

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency–Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research

Defect dynamics in polycrystalline zirconium alloy probed in situ by primary extinction of neutron diffraction

After alpha+beta-zirconium has fully transformed into beta-phase upon heating, the intensities of all beta-Zr Bragg reflections decrease simultaneously as a function of time. It is shown that this effect represents a transition from the kinematic to the dynamic theory of diffraction due to the ever increasing crystal perfection driven by thermal recovery of the system. The best fitting coherent crystallite size of 30 mu m and other microstructural features are verified by in situ laser scanning confocal microscopy. This effect of primary extinction in neutron diffraction has been employed to further investigate the crystal perfection kinetics. Upon further heating, crystal recovery is identified as a process of dislocation annihilation, suffering from lattice friction. Upon cooling, precipitating alpha-Zr induces strain into the perfect beta-crystallites, re-establishing the kinematic diffraction intensities. An Avrami analysis leads to the estimations of nucleation time, consumption of nucleation sites and lower-dimensional growth. Such technique bears great value for further investigation on all metal systems annealed close to the melting temperature. © 2013, American Institute of Physics

In-situ characterization of lattice structure evolution during phase transformation of Zr-2.5Nb

The alpha-beta phase transformation behavior of Zr-2.5Nb (in mass%) has been characterized in real time during an in situ neutron diffraction experiment. The Zr-2.5Nb material in the current study consists, at room temperature, of alpha-Zr phase (hcp) and two beta phases (bcc), a Nb rich beta-Nb phase and retained, Zr rich, beta-Zr(Nb) phase. It is suggested that this is related to a quench off the equilibrium solubility of Nb atoms in the Zr bcc unit cells. Vegard's law combined with thermal expansion is applied to calculate the composition of the beta-phase, which is compared with the phase diagram, revealing the system's kinetic behavior for approaching equilibrium. © 2011, Wiley-Blackwell. The definitive version is available at www3.interscience.wiley.co