Distinct transcriptional roles for Histone H3-K56 acetylation during the cell cycle in Yeast

Dynamic disruption and reassembly of promoter-proximal nucleosomes is a conserved hallmark of transcriptionally active chromatin. Histone H3-K56 acetylation (H3K56Ac) enhances these turnover events and promotes nucleosome assembly during S phase. Here we sequence nascent transcripts to investigate the impact of H3K56Ac on transcription throughout the yeast cell cycle. We find that H3K56Ac is a genome-wide activator of transcription. While H3K56Ac has a major impact on transcription initiation, it also appears to promote elongation and/or termination. In contrast, H3K56Ac represses promiscuous transcription that occurs immediately following replication fork passage, in this case by promoting efficient nucleosome assembly. We also detect a stepwise increase in transcription as cells transit S phase and enter G2, but this response to increased gene dosage does not require H3K56Ac. Thus, a single histone mark can exert both positive and negative impacts on transcription that are coupled to different cell cycle events

INO80C Remodeler Maintains Genomic Stability by Preventing Promiscuous Transcription at Replication Origins

The proper coordination of transcription with DNA replication and repair is central for genomic stability. We investigate how the INO80C chromatin remodeling enzyme might coordinate these genomic processes. We find that INO80C co-localizes with the origin recognition complex (ORC) at yeast replication origins and is bound to replication initiation sites in mouse embryonic stem cells (mESCs). In yeast, INO80C recruitment requires origin sequences but does not require ORC, suggesting that recruitment is independent of pre-replication complex assembly. In both yeast and ESCs, INO80C co-localizes at origins with Mot1 and NC2 transcription factors, and genetic studies suggest that they function together to promote genome stability. Interestingly, nascent transcript sequencing demonstrates that INO80C and Mot1 prevent pervasive transcription through origin sequences, and absence of these factors leads to formation of new DNA double-strand breaks. We propose that INO80C and Mot1/NC2 function through distinct pathways to limit origin transcription, maintaining genomic stability

CO Tully–Fisher relation of star-forming galaxies at = 0.05–0.3

The Tully–Fisher relation (TFR) is an empirical relation between galaxy luminosity and rotation velocity. We present here the first TFR of galaxies beyond the local Universe that uses carbon monoxide (CO) as the kinematic tracer. Our final sample includes 25 isolated, non-interacting star-forming galaxies with double-horned or boxy CO integrated line profiles located at redshifts z ≤ 0.3, drawn from a larger ensemble of 67 detected objects. The best reverse Ks-band, stellar mass and baryonic mass CO TFRs are, respectively, MKs = (−8.4 ± 2.9)[log ( W50/km s−1 sin i ) − 2.5] + (−23.5 ± 0.5), log (M/M) = (5.2 ± 3.0)[log ( W50/km s−1 sin i ) − 2.5] + (10.1 ± 0.5) and log (Mb/M) = (4.9 ± 2.8)[log ( W50/km s−1 sin i ) − 2.5] + (10.2 ± 0.5), where MKs is the total absolute Ks-band magnitude of the objects, M and Mb their total stellar and baryonic masses, and W50 the width of their line profile at 50 per cent of the maximum. Dividing the sample into different redshift bins and comparing to the TFRs of a sample of local (z = 0) star-forming galaxies from the literature, we find no significant evolution in the slopes and zero-points of the TFRs since z ≈ 0.3, this in either luminosity or mass. In agreement with a growing number of CO TFR studies of nearby galaxies, we more generally find that CO is a suitable and attractive alternative to neutral hydrogen (HI). Our work thus provides an important benchmark for future higher redshift CO TFR studies

Amino Acid Substitutions at Position 43 of Nae I Endonuclease: EVIDENCE FOR CHANGES INNaeI STRUCTURE

NaeI endonuclease contains a 10-amino acid region with sequence similarity to the active site KXDG motif of DNA ligase except for leucine (Leu-43) in NaeI ((43)LXDG(46)). Changing Leu-43 to lysine abolishes the NaeI endonuclease activity and replaces it with topoisomerase and recombinase activities. Here we report the results of substituting Leu-43 with alanine, arginine, asparagine, glutamate, and histidine. Quantitating specific activities and DNA binding values for the mutant proteins determined the range of amino acids at position 43 that alter NaeI mechanism. Substituting alanine, asparagine, glutamate, and histidine for Leu-43 maintained endonuclease activity, but at a lower level. On the other hand, substituting positively charged arginine, like lysine at position 43, converted NaeI to a topoisomerase with no observable double-strand cleavage activity. The specific activities of NaeI-43K and NaeI-43R and their relative sensitivities to salt, the topoisomerase-inhibiting drug N-[4-(9-acridinylamino)-3-methoxyphenyl]methane-sulfonamide (amsacrine) and single-stranded DNA showed that the two activities are similar. The effect of placing a positive charge at position 43 on NaeI structure was determined by measuring (for NaeI and NaeI-43K) relative susceptibilities to proteolysis, UV, circular dichroism spectra, and temperature melting transitions. The results provide evidence that a positive charge at position 43 induces dramatic changes in NaeI structure that affect both the Endo and Topo domains of NaeI. The identification of four putative DNA ligase motifs in NaeI leads us to speculate that structural changes that superimpose these motifs on the ligase structure may account for the changes in activity

Triplet Repeat Expansion Generated by DNA Slippage Is Suppressed by Human Flap Endonuclease 1

Human flap endonuclease 1 (h-FEN1) mutations have dramatic effects on repeat instability. Current models for repeat expansion predict that h-FEN1 protein prevents mutations by removing 5'-flaps generated at ends of Okazaki fragments by strand displacement synthesis. The models propose that hairpin formations within flaps containing repeats enable them to escape h-FEN1 cleavage. Friedreich's ataxia is caused by expansion mutations in a d(GAA)n repeat tract. Single-stranded d(GAA)n repeat tracts, however, do not form stable hairpins until the repeat tracts are quite long. Therefore, to understand how d(GAA)n repeat expansions survive h-FEN1 activity, we determined the effects of h-FEN1 on d(GAA)n repeat expansion during replication of a d(TTC)n repeat template. Replication initiated within the repeat tract generated significant expansion that was suppressed by the addition of h-FEN1 at the start of replication. The ability of h-FEN1 to suppress expansion implies that DNA slippage generates a 5'-flap in the nascent strand independent of strand displacement synthesis by an upstream polymerase. Delaying the addition of h-FEN1 to the replication reaction abolished the ability of h-FEN1 ability to suppress d(GAA)n repeat expansion products of all sizes, including sizes unable to hairpin. Use of model substrates demonstrated that h-FEN1 cleaves d(GAA)n 5'-flaps joined to double-stranded nonrepeat sequences but not those joined to double-stranded repeat tracts. The results provide evidence that, given the opportunity, short d(GAA)n repeat expansion products rearrange from 5'-flaps to stable internal loops inside the repeat tract. Long expansion products are predicted to form hairpinned flaps and internal loops. Once formed, these DNA conformations resist h-FEN1. The biological implications of the results are discussed

Laboratory comparison of aging characteristics of warm mix asphalts involving natural and synthetic water containing additives

When comparing the aging characteristics of hot and warm mix asphalts from a technical point of view, it can intuitively be expected that a warm mix asphalt would be less subjected to aging-induced failures due to lower application temperatures. Since the side effects of warm asphalt technology should be investigated distinctly. This study addresses the aging investigation of properties of bituminous mixtures containing two (i.e., natural and synthetic zeolite) water based additives available on the market. Within the scope of this study, short- and long-term aging conditions were simulated on mixtures containing various contents of additives as well as on control specimens. The aging indices were determined based on the hardness ratio employing indirect tensile strength values in order to investigate the aging induced failures betide by time. Aging indices showed that the specimens with water containing additives demonstrate relatively better resistance against hardening than conventional hot mix asphalt specimens

Дослідження потужності електричної активності утворень мозку за умов пілокарпін-індукованої спонтанної судомної активності = The investigation of brain structures magnitude in conditios of pilocarpine-induced spontaneous activity

Kopyova N. V., Lyashenko S. L., Topal M. M. Дослідження потужності електричної активності утворень мозку за умов пілокарпін-індукованої спонтанної судомної активності = The investigation of brain structures magnitude in conditios of pilocarpine-induced spontaneous activity. Journal of Education, Health and Sport. 2015;5(8):159-176. ISSN 2391-8306. DOI 10.5281/zenodo.28046http://dx.doi.org/10.5281/zenodo.28046http://ojs.ukw.edu.pl/index.php/johs/article/view/2015%3B5%288%29%3A159-176https://pbn.nauka.gov.pl/works/607585Formerly Journal of Health Sciences. ISSN 1429-9623 / 2300-665X. Archives 2011–2014 http://journal.rsw.edu.pl/index.php/JHS/issue/archive Deklaracja.Specyfika i zawartość merytoryczna czasopisma nie ulega zmianie.Zgodnie z informacją MNiSW z dnia 2 czerwca 2014 r., że w roku 2014 nie będzie przeprowadzana ocena czasopism naukowych; czasopismo o zmienionym tytule otrzymuje tyle samo punktów co na wykazie czasopism naukowych z dnia 31 grudnia 2014 r.The journal has had 5 points in Ministry of Science and Higher Education of Poland parametric evaluation. Part B item 1089. (31.12.2014).© The Author (s) 2015;This article is published with open access at Licensee Open Journal Systems of Kazimierz Wielki University in Bydgoszcz, Poland and Radom University in Radom, PolandOpen Access. This article is distributed under the terms of the Creative Commons Attribution Noncommercial License which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and source are credited. This is an open access article licensed under the terms of the Creative Commons Attribution Non Commercial License (http://creativecommons.org/licenses/by-nc/3.0/) which permits unrestricted, non commercial use, distribution and reproduction in any medium, provided the work is properly cited.This is an open access article licensed under the terms of the Creative Commons Attribution Non Commercial License (http://creativecommons.org/licenses/by-nc/3.0/) which permits unrestricted, non commercialuse, distribution and reproduction in any medium, provided the work is properly cited.The authors declare that there is no conflict of interests regarding the publication of this paper.Received: 05.06.2015. Revised 15.07.2015. Accepted: 12.08.2015. УДК 612.017.1:612.8.062;612.821.7+616.853 ДОСЛІДЖЕННЯ ПОТУЖНОСТІ ЕЛЕКТРИЧНОЇ АКТИВНОСТІ УТВОРЕНЬ МОЗКУ ЗА УМОВ ПІЛОКАРПІН-ІНДУКОВАНОЇ СПОНТАННОЇ СУДОМНОЇ АКТИВНОСТІTHE INVESTIGATION OF BRAIN STRUCTURES MAGNITUDE IN CONDITIOS OF PILOCARPINE-INDUCED SPONTANEOUS ACTIVITY Н. В. Копйова, С. Л. Ляшенко, *М. М. ТопалN. V. Kopyova, S. L. Lyashenko, *M. M. Topal Одеський національний медичний університет, Одеса; *Одеський національний університет ім. І. І. Мечникова, ОдесаOdessa National Medical University, Odessa; *Odessa I. I. Mechnikov National University, Odessa SummaryThe article deals with the results of the trials devoted to pilocarpine-induced spontaneous seizure activity pathophysiologic mechanisms investigation. With this aim the main factors determining spontaneous seizure onset were studied as well as hippocampus and frontal cortex pathogenetic role was investigated in conditions pilocarpine-induced chronic epileptogenesis. Status epilepticus development and its duration were shown to be the main factors determining pilocarpine-induced spontaneous seizures. Hippocampal hyperactivation was found to precede the spontaneous seizures formation that afterwards followed by the brain frontal cortex f the electrical activity strengthening. These brain structures electrical activity hyperactivation occurs due to a- and d-rhythms.Key words: pilocarpine, spontaneous seizures, the hippocampus, cerebral cortex, the power of the electrical activity, pathophysiologic mechanisms. РезюмеВ роботі наведені результати досліджень, присвячених з'ясуванню патофізіологічних механізмів спонтанної судомної активності, індукованої введенням пілокарпіну. З цією метою вивчали основні чинники, що визначають розвиток спонтанних судом, а також з'ясовували патогенетичну роль гіпокампу і фронтальної кори в умовах пілокарпін-викликаного хронічного епілептогенезу. Показано, що розвиток епілептичного статусу, а також його тривалість детермінують формування спонтанних пілокарпін-викликаних судомних реакцій. Визначено, що формуванню спонтанних судом передує гіперактивація нейронів гіпокампу, слід за чим посилюється електрична активність фронтальної кори мозку. Посилення електричної активності зазначених утворень мозку відбувається за рахунок a- та d-діапазонів.Ключові слова: пілокарпін, спонтанні судоми, гіпокамп, кора мозку, потужність електричної активності, патофізіологічні механізми. РезюмеИЗУЧЕНИЕ МОЩНОСТИ ЭЛЕКТРИЧЕСКОЙ АКТИВНОСТИ СТРУКТУР МОЗГА В УСЛОВИЯХ ПИЛОКАРПИН-ИНДУЦИРОВАННОЙ СПОНТАННОЙ СУДОРОЖНОЙ АКТИВНОСТИ. В работе приведены результаты исследований, посвященных выяснению патофизиологических механизмов спонтанной судорожной активности, индуцированной введением пилокарпина. С этой целью изучали основные факторы, определяющие развитие спонтанных судорог, а также выясняли патогенетическую роль гиппокампа и фронтальной коры в условиях пилокарпин-вызванного хронического эпилептогенеза. Показано, что развитие эпилептического статуса, а также его продолжительность детерминируют формирование спонтанных пилокарпин-вызванных судорожный реакций. Выяснено, что формированию спонтанных судорог предшествует гиперактивация нейронов гиппокампа, за которой потом следует усиление электрической активности фронтальной коры мозга. Усиление электрической активности отмеченных структур мозга происходит за счет a- и d-диапазонов.Ключевые слова: пилокарпин, спонтанные судороги, гиппокамп, кора мозга, мощность электрической активности, патофизиологические механизмы

Hairpin Formation in Friedreich's Ataxia Triplet Repeat Expansion

Triplet repeat tracts occur throughout the human genome. Expansions of a (GAA)(n)/(TTC)(n) repeat tract during its transmission from parent to child are tightly associated with the occurrence of Friedreich's ataxia. Evidence supports DNA slippage during DNA replication as the cause of the expansions. DNA slippage results in single-stranded expansion intermediates. Evidence has accumulated that predicts that hairpin structures protect from DNA repair the expansion intermediates of all of the disease-associated repeats except for those of Friedreich's ataxia. How the latter repeat expansions avoid repair remains a mystery because (GAA)(n) and (TTC)(n) repeats are reported not to self-anneal. To characterize the Friedreich's ataxia intermediates, we generated massive expansions of (GAA)(n) and (TTC)(n) during DNA replication in vitro using human polymerase beta and the Klenow fragment of Escherichia coli polymerase I. Electron microscopy, endonuclease cleavage, and DNA sequencing of the expansion products demonstrate, for the first time, the occurrence of large and growing (GAA)(n) and (TTC)(n) hairpins during DNA synthesis. The results provide unifying evidence that predicts that hairpin formation during DNA synthesis mediates all of the disease-associated, triplet repeat expansions