354 research outputs found
Study of a novel evolutionarily conserved pattern of histone acetylation
Le gĂ©nome eucaryote est empaquetĂ© dans une structure hautement ordonnĂ©e appelĂ©e chromatine. MĂȘme si la structure de la chromatine est importante pour le maintien de l'intĂ©gritĂ© gĂ©nomique, elle constitue une barriĂšre Ă de nombreux processus basĂ©s sur l'ADN tels que la rĂ©plication de l'ADN, la transcription et la rĂ©paration de l'ADN. Les histones contiennent une diversitĂ© dĂ©concertante de modifications covalentes qui sont concentrĂ©es principalement, mais non exclusivement dans leurs queues amino-terminales. Les modifications des histones jouent un rĂŽle central dans la rĂ©gulation de la structure et de la fonction de la chromatine. Cependant, la dĂ©termination de la stoechiomĂ©trie des modifications Ă des sites spĂ©cifiques, l'identification des motifs de modifications et l'Ă©tablissement de leurs rĂŽles physiologiques restent des dĂ©fis redoutables.
Dans cette Ă©tude, nous avons utilisĂ© la spectromĂ©trie de masse pour dĂ©terminer la stoechiomĂ©trie de l'acĂ©tylation de rĂ©sidus lysine spĂ©cifiques des histones. En gĂ©nĂ©ral, les rĂ©sidus lysine des histones dĂ©pourvus d'acĂ©tylation sont dĂ©rivatisĂ©s pour rendre les peptides rĂ©sultants chimiquement Ă©quivalents Ă leurs homologues acĂ©tylĂ©s, mais pouvant ĂȘtre distinguĂ©s par spectromĂ©trie de masse. Cependant, cette mĂ©thode est insuffisante pour Ă©tudier les peptides contenant plus d'une lysine acĂ©tylable, tels que ceux dĂ©rivĂ©s de la queue N-terminale des histones H3 et H4. La digestion trypsique de tels peptides gĂ©nĂšre des «isomĂšres de position», des isomĂšres qui ont la mĂȘme masse, mais qui portent des groupes acĂ©tyle Ă des positions diffĂ©rentes. La quantification prĂ©cise de l'acĂ©tylation d'un site spĂ©cifique dans ces peptides est donc un dĂ©fi analytique majeur.
Dans le deuxiĂšme chapitre, nous dĂ©crivons une nouvelle mĂ©thode, pour quantifier l'acĂ©tylation Ă un site spĂ©cifique dans les peptides co-Ă©luants isomĂ©riques et isobariques, qui combine des donnĂ©es LC-MS / MS Ă haute rĂ©solution avec un nouvel algorithme bioinformatique, Iso-PeptidAce. En utilisant des spectres de masse en tandem (MS/MS) de peptides synthĂ©tiques, les produits de fragmentation caractĂ©ristiques de chaque isomĂšre de position ont Ă©tĂ© identifiĂ©s et utilisĂ©s pour dĂ©convoluer des spectres provenant de mĂ©langes d'isomĂšres de position et quantifier l'abondance de chaque isomĂšre. Nous avons ensuite testĂ© l'applicabilitĂ© de l'Iso-PeptidAce pour quantifier les augmentations en fonction du temps de l'acĂ©tylation des histones des cellules d'Ă©rythroleucĂ©mie K562 traitĂ©es avec des inhibiteurs dâhistone dĂ©acĂ©tylase (HDAC). En utilisant notre mĂ©thode, nous avons Ă©galement trouvĂ© que les histones H3 et H4 associĂ©es Ă CAF-1, un facteur d'assemblage de la chromatine, ont une stoechiomĂ©trie Ă©levĂ©e dâacĂ©tylation sur plusieurs rĂ©sidus de H3 et H4, par rapport aux histones totales.
Dans le chapitre 3, nous avons appliquĂ© Iso-PeptidAce pour dĂ©terminer la stoechiomĂ©trie de l'acĂ©tylation chez la levure de fission prĂ©sentant un mutant dâhistone dĂ©sacĂ©tylase. ConformĂ©ment aux Ă©tudes antĂ©rieures impliquant Clr3 et Sir2 dans la rĂ©gulation de lâhĂ©tĂ©rochromatine, nous avons observĂ© que les cellules dĂ©pourvues de ces HDAC prĂ©sentaient une augmentation de l'acĂ©tylation H3-K14 uniquement sur les peptides coexistant avec H3-K9 di / tri mĂ©thylĂ©, une marque caractĂ©ristique de l'hĂ©tĂ©rochromatine.
Au chapitre 4, nous dĂ©crivons la dĂ©couverte de trĂšs hauts niveaux d'acĂ©tylation sur deux rĂ©sidus de lysine. Nous avons trouvĂ© qu'une stoechiomĂ©trie Ă©levĂ©e dâacĂ©tylation Ă H3-K14 et H3-K23 et une faible stoechiomĂ©trie dâacĂ©tylation Ă H3-K9 et H3-K18 est un profil global de H3 conservĂ© sur le plan Ă©volutif dâacĂ©tylation. En utilisant des souches de levures de fission (S. pombe) oĂč la seule source de gĂšnes d'histone porte des mutations H3-K14R et / ou H3-K23R qui empĂȘchent l'acĂ©tylation, nous avons dĂ©montrĂ© que H3-K14 et H3-K23 ont des fonctions distinctes. De façon surprenante, nous avons trouvĂ© que les phĂ©notypes observĂ©s dans les cellules mutantes H3-K14R sont largement dus Ă la mutation du rĂ©sidu lysine, plutĂŽt qu'Ă la perte d'acĂ©tylation. En utilisant des souches de S. pombe dĂ©pourvues d'histone acĂ©tyltransfĂ©rases (HAT), nous avons identifiĂ© les acĂ©tyltransfĂ©rases qui contribuent Ă H3-K14ac et Ă H3-K23ac in vivo.
TrĂšs peu d'Ă©tudes ont cherchĂ© Ă dĂ©terminer spĂ©cifiquement les stoechiomĂ©tries d'acĂ©tylation des histones. Nos rĂ©sultats suggĂšrent quâen moyenne, sur l'ensemble du gĂ©nome, chaque deuxiĂšme ou troisiĂšme nuclĂ©osome contient une molĂ©cule H3 avec une acĂ©tylation K14 et / ou K23. Cela nous amĂšne Ă penser que l'acĂ©tylation de l'histone H3 Ă l'Ă©chelle du gĂ©nome peut jouer un rĂŽle important dans la fonction chromosomique. Il est impĂ©ratif de comprendre la signification fonctionnelle de ce modĂšle d'acĂ©tylation Ă©tant donnĂ© que la thĂ©rapie Ă©pigĂ©nĂ©tique est activement Ă©tudiĂ©e comme stratĂ©gie pour traiter de nombreuses maladies.The eukaryotic genome is packaged into a highly ordered chromatin structure. Even though chromatin structure is important for maintaining genomic integrity, it is a barrier to numerous DNA-based processes such as DNA replication, transcription and DNA repair. Histones contain a bewildering diversity of covalent modifications that are mostly but not exclusively concentrated within their amino-terminal tails. Histone modifications play a central role in regulating chromatin structure and function. However, determining the stoichiometry of site-specific modifications, identifying patterns of modifications and establishing their physiological roles remain formidable challenges.
In this study, we exploited mass spectrometry to determine the stoichiometry of acetylation at specific histone lysine residues. In general, histone lysine residues lacking acetylation are derivatized to render the resulting peptides chemically equivalent but distinguishable by mass from their acetylated counterparts. However, this method is insufficient to study peptides that contain more than one acetylatable lysine, such as those derived from the N-terminal tail of histones H3 and H4. Tryptic digestion of such peptides generates âpositional isomersâ, isomers that have the same mass but bearing acetyl groups located at different positions. Accurate quantification of site-specific acetylation in those peptides is, therefore, a major analytical challenge.
In the second chapter, we describe a novel method for quantifying site-specific acetylation of co-eluting isomeric and isobaric peptides that combines high-resolution LC-MS/MS data with a novel bioinformatics algorithm, Iso-PeptidAce. Using tandem mass spectra (MS/MS) of synthetic peptides, fragmentation products diagnostic of each positional isomer were identified and were used to deconvolute spectra that arise from mixtures of positional isomers and quantify the abundance of each isomer. We then tested the applicability of Iso-PeptidAce to quantify time-dependent increases in histone acetylation of K562 erythroleukaemia cells treated with histone deacetylase (HDAC) inhibitors. Using our method, we also found that histones H3 and H4 associated with CAF-1, a chromatin assembly factor, have a high stoichiometry of acetylation on multiple residues of H3 and H4, compared with total histones.
In Chapter 3, we applied Iso-PeptidAce to determine the stoichiometry of acetylation in fission yeast histone deacetylase mutants. Consistent with previous reports implicating Clr3 and Sir2 in heterochromatin function, we observed that cells lacking these HDACs showed an increase in H3-K14 acetylation only on those peptides where it co-exists with di/trimethylated H3-K9, a mark of heterochromatin.
In chapter 4, we describe the discovery of very high levels of acetylation on two lysine residues. We found that a high stoichiometry of acetylation at H3-K14 and H3-K23, and low stoichiometry of acetylation at H3-K9 and H3-K18, is an evolutionarily conserved global pattern of H3 acetylation. Using fission yeast (S. pombe) strains harboring histone mutations H3-K14R and/or H3-K23R that prevent acetylation, we demonstrate that H3-K14 and H3-K23 have separable functions. Surprisingly, we found that the phenotypes observed in H3-K14R mutant cells are largely due to mutation of the lysine residue, rather than loss of acetylation. Using S. pombe strains that lack histone acetyltransferases (HATs) we identified the acetyltransferases that contribute to H3-K14ac and H3-K23ac in vivo.
Very few studies have aimed at specifically determining the acetylation stoichiometries of histones. Our results suggest that, on average, over the entire genome, every second or third nucleosome contains an H3 molecule with K14 and/or K23 acetylation. This leads us to surmise that genome-wide acetylation of histone H3 may have an important role in chromosome function. It is imperative to understand the functional significance of this acetylation pattern given that epigenetic therapy is actively pursued as a strategy to treat many diseases
Tuberculosis and metastatic carcinoma coexistence in axillary lymph node: A case report
BACKGROUND: Coexistence of cancer and tuberculosis in axillary lymph nodes is rare. Only seven cases have been reported in the literature. CASE REPORT: We report here a case of infiltrating ductal carcinoma breast metastasizing to the axillary lymph node along with tubercular granuloma in the same lymph node without primary mammary or pulmonary tuberculosis. CONCLUSION: Primary tuberculosis coexisting with carcinoma is of rare occurrence. A possibility should always be borne in mind especially in patients from endemic areas
Optical Properties of High-Frequency Radio Sources from the Australia Telescope 20 GHz (AT20G) Survey
Our current understanding of radio-loud AGN comes predominantly from studies
at frequencies of 5 GHz and below. With the recent completion of the Australia
Telescope 20 GHz (AT20G) survey, we can now gain insight into the
high-frequency radio properties of AGN. This paper presents supplementary
information on the AT20G sources in the form of optical counterparts and
redshifts. Optical counterparts were identified using the SuperCOSMOS database
and redshifts were found from either the 6dF Galaxy survey or the literature.
We also report 144 new redshifts. For AT20G sources outside the Galactic plane,
78.5% have optical identifications and 30.9% have redshift information. The
optical identification rate also increases with increasing flux density.
Targets which had optical spectra available were examined to obtain a spectral
classification.
There appear to be two distinct AT20G populations; the high luminosity
quasars that are generally associated with point-source optical counterparts
and exhibit strong emission lines in the optical spectrum, and the lower
luminosity radio galaxies that are generally associated with passive galaxies
in both the optical images and spectroscopic properties. It is suggested that
these different populations can be associated with different accretion modes
(cold-mode or hot-mode). We find that the cold-mode sources have a steeper
spectral index and produce more luminous radio lobes, but generally reside in
smaller host galaxies than their hot-mode counterparts. This can be attributed
to the fact that they are accreting material more efficiently. Lastly, we
compare the AT20G survey with the S-cubed semi-empirical (S3-SEX) models and
conclude that the S3-SEX models need refining to correctly model the compact
cores of AGN. The AT20G survey provides the ideal sample to do this.Comment: Accepted for publication in MNRA
In Situ Recrystallization of Co-Evaporated Cu(In,Ga)Se\u3csub\u3e2\u3c/sub\u3e Thin Films by Copper Chloride Vapor Treatment Towards Solar Cell Applications
Cu(In,Ga)Se2 (or CIGS) thin films and devices were fabricated using a modified three-stage process. Using high deposition rates and a low temperature during the process, a copper chloride vapor treatment was introduced in between the second and third stages to enhance the films properties. X-ray diffraction and scanning electron microscopy demonstrate that drastic changes occur after this recrystallization process, yielding films with much larger grains. Secondary ion mass spectrometry shows that the depth profile of many elements is not modified (such as Cu, In and Se) while others change dramatically (such as Ga and Na). Because of the competing effects of these changes, not all parameters of the solar cells are enhanced, yielding an increase of 15% in the device efficiency at the most
Learning without contingencies induces higher order asynchrony in brain networks in schizophrenia
Schizophrenia (SCZ) is characterized by both cognitive and reward impairments. A recent study suggests that SCZ is associated with a loss of synchrony between learning and reward circuits (Robison et al., 2019) and higher levels of dis-organization of functional brain networks may underpin failures in learning that characterize SCZ (HĂŒtt et al., 2014). Therefore, here we examined inter-group (HC â SCZ) 4th order differences in statistical regularity across a connectome of cognition and reward brain circuits. The analyses were conducted on fMRI time series data from a previous learning paradigm (Stanley et al., 2017) with periods of Encoding and Retrieval. 75 participants (46 SCZ, 18 Age 50) consented for fMRI. Time Series were extracted from eight bilateral a priori nodes (across learning and reward sub-networks). 2nd order undirectional functional connectivity was characterized across all nodal pairs during Encoding, Retrieval, and their subsequent rest periods. From this, a 4th order cross-correlation matrix was produced within each group and condition. Significant 4th order differences were projected to chords in the 4th order connectomic rings for Encoding and Retrieval (Figure 1). Two effects are evident: 1) SCZ are characterized by a massive loss of 4th order synchrony during both Encoding and Retrieval and 2) Retrieval evokes a greater loss in 4th order statistical synchrony than does Encoding. These results appear to validate the idea the SCZ is characterized by a loss of synergy between cognition and reward circuits, and that this loss of synergy is evident at higher order scales
The Australia Telescope 20GHz (AT20G) Survey: analysis of the extragalactic source sample
The Australia Telescope 20 GHz (AT20G) survey is a blind survey of the whole
Southern sky at 20 GHz with follow-up observations at 4.8, 8.6, and 20 GHz
carried out with the Australia Telescope Compact Array (ATCA). In this paper we
present an analysis of radio spectral properties in total intensity and
polarisation, sizes, optical identifications, and redshifts of the sample of
the 5808 extragalactic sources in the survey catalogue of confirmed sources
over the whole Southern sky excluding the strip at Galactic latitude
|b|<1.5deg. The sample has a flux density limit of 40 mJy. Completeness has
been measured as a function of scan region and flux density. Averaging over the
whole survey area the follow-up survey is 78% complete above 50mJy and 93%
complete above 100mJy. 3332 sources with declination <-15deg have good quality
almost simultaneous observations at 4.8, 8.6, and 20GHz. The spectral analysis
shows that the sample is dominated by flat-spectrum sources. The fraction of
flat-spectrum sources decreases from 81% for 20GHz flux densities S>500mJy, to
60% for S<100mJy. There is also a clear spectral steepening at higher
frequencies with the median spectral index decreasing from -0.16 between 4.8
and 8.6GHz to -0.28 between 8.6 and 20GHz. Simultaneous observations in
polarisation are available for all the sources at all the frequencies. 768
sources have a good quality detection of polarised flux density at 20GHz; 467
of them were also detected in polarisation at 4.8 and/or at 8.6GHz so that it
has been possible to compare the spectral behaviour in total intensity and
polarisation. We have found that the polarised fraction increases slightly with
frequency and decreases with flux density. Cross matches and comparisons have
been made with other catalogues at lower radio frequencies, and in the optical,
X-ray and gamma-ray bands. Redshift estimates are available for 825 sources.Comment: 15 pages, 16 figures, accepted for publication in MNRA
An Erythropoietin-Independent Mechanism of Erythrocytic Precursor Proliferation Underlies Hypoxia Tolerance in Sea Nomads
The Bajau Sea Nomads were recently demonstrated to have evolved larger spleens as an adaptation to millennia of a marine foraging lifestyle. The large-spleen phenotype appears to derive from increases in thyroid hormone (TH) production as a result of reduced expression of phosphodiesterase 10A (PDE10A), though the exact mechanism remains unknown. Through pharmacological inhibition of PDE10A using the selective inhibitor MP-10 in mice, we were able to mimic the Bajau adaptation and show that treated mice had significantly larger spleens than control animals. This difference appears connected to an excess of early stage erythrocytes and an apparent increase in red blood cell (RBC) precursor proliferation in response to increased TH. However, we determined that the stimulation of RBC production in the mouse model via TH is Erythropoietin (EPO)-independent, unlike in the altitude (chronic hypoxemia) response. We confirmed this using human GWAS data; although the Bajau PDE10A variants are significantly associated with increased TH levels and RBC count, they are not associated with EPO levels, nor are other strongly thyroid-associated SNPs. We therefore suggest that an EPO-independent mechanism of stimulating RBC precursor proliferation via TH upregulation underlies the increase in spleen size observed in Sea Nomad populations
Exosomal microRNAs in breast cancer: towards theranostic applications
Breast cancer is one of the top two reproductive cancers responsible for high rates of morbidity and mortality among women globally. Despite the advancements in the treatment of breast cancer, its early diagnosis remains a challenge. Recent evidence indicates that despite the adroit use of numerous strategies to facilitate rapid and precision-oriented screening of breast cancer at the community level through the use of mammograms, Fine-needle aspiration cytology (FNAC) and biomarker tracking, no strategy has been unequivocally accepted as a gold standard for facilitating rapid screening for disease. This necessitates the need to identify novel strategies for the detection and triage of breast cancer lesions at higher rates of specificity, and sensitivity, whilst taking into account the epidemiologic and social-demographic features of the patients. Recent shreds of evidence indicate that exosomes could be a robust source of biomaterial for the rapid screening of breast cancer due to their high stability and their presence in body fluids. Increasing evidence indicates that the Exosomal microRNAs- play a significant role in modifying the tumour microenvironment of breast cancers, thereby potentially aiding in the proliferation, invasion and metastasis of breast cancer. In this review, we summarize the role of ExomiRs in the tumour microenvironment in breast cancer. These ExomiRs can also be used as candidate biomarkers for facilitating rapid screening and triaging of breast cancer patients for clinical intervention
- âŠ