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1.
Brandon S. Sheffield Anna V. Tinker Yaoqing Shen Harry Hwang Hector H. Li-Chang Erin Pleasance Carolyn Ch’ng Amy Lum Julie Lorette Yarrow J. McConnell Sophie Sun Steven J. M. Jones Allen M. Gown David G. Huntsman David F. Schaeffer Andrew Churg Stephen Yip Janessa Laskin Marco A. Marra 《PloS one》2015,10(3)
Peritoneal mesothelioma is a rare and sometimes lethal malignancy that presents a clinical challenge for both diagnosis and management. Recent studies have led to a better understanding of the molecular biology of peritoneal mesothelioma. Translation of the emerging data into better treatments and outcome is needed. From two patients with peritoneal mesothelioma, we derived whole genome sequences, RNA expression profiles, and targeted deep sequencing data. Molecular data were made available for translation into a clinical treatment plan. Treatment responses and outcomes were later examined in the context of molecular findings. Molecular studies presented here provide the first reported whole genome sequences of peritoneal mesothelioma. Mutations in known mesothelioma-related genes NF2, CDKN2A, LATS2, amongst others, were identified. Activation of MET-related signaling pathways was demonstrated in both cases. A hypermutated phenotype was observed in one case (434 vs. 18 single nucleotide variants) and was associated with a favourable outcome despite sarcomatoid histology and multifocal disease. This study represents the first report of whole genome analyses of peritoneal mesothelioma, a key step in the understanding and treatment of this disease. 相似文献
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E. W. N. Stevens J. V. Bailey B. E. Flood D. S. Jones W. P. Gilhooly III S. B. Joye A. Teske O. U. Mason 《Geobiology》2015,13(6):588-603
Crusts and chimneys composed of authigenic barite are found at methane seeps and hydrothermal vents that expel fluids rich in barium. Microbial processes have not previously been associated with barite precipitation in marine cold seep settings. Here, we report on the precipitation of barite on filaments of sulfide‐oxidizing bacteria at a brine seep in the Gulf of Mexico. Barite‐mineralized bacterial filaments in the interiors of authigenic barite crusts resemble filamentous sulfide‐oxidizing bacteria of the genus Beggiatoa. Clone library and iTag amplicon sequencing of the 16S rRNA gene show that the barite crusts that host these filaments also preserve DNA of Candidatus Maribeggiatoa, as well as sulfate‐reducing bacteria. Isotopic analyses show that the sulfur and oxygen isotope compositions of barite have lower δ34S and δ18O values than many other marine barite crusts, which is consistent with barite precipitation in an environment in which sulfide oxidation was occurring. Laboratory experiments employing isolates of sulfide‐oxidizing bacteria from Gulf of Mexico seep sediments showed that under low sulfate conditions, such as those encountered in brine fluids, sulfate generated by sulfide‐oxidizing bacteria fosters rapid barite precipitation localized on cell biomass, leading to the encrustation of bacteria in a manner reminiscent of our observations of barite‐mineralized Beggiatoa in the Gulf of Mexico. The precipitation of barite directly on filaments of sulfide‐oxidizing bacteria, and not on other benthic substrates, suggests that sulfide oxidation plays a role in barite formation at certain marine brine seeps where sulfide is oxidized to sulfate in contact with barium‐rich fluids, either prior to, or during, the mixing of those fluids with sulfate‐containing seawater in the vicinity of the sediment/water interface. As with many other geochemical interfaces that foster mineral precipitation, both biological and abiological processes likely contribute to the precipitation of barite at marine brine seeps such as the one studied here. 相似文献
4.
Luis J. García-Rodríguez Giacomo De?Piccoli Vanessa Marchesi Richard C. Jones Ricky D. Edmondson Karim Labib 《Nucleic acids research》2015,43(18):8830-8838
Defects during chromosome replication in eukaryotes activate a signaling pathway called the S-phase checkpoint, which produces a multifaceted response that preserves genome integrity at stalled DNA replication forks. Work with budding yeast showed that the ‘alternative clamp loader’ known as Ctf18-RFC acts by an unknown mechanism to activate the checkpoint kinase Rad53, which then mediates much of the checkpoint response. Here we show that budding yeast Ctf18-RFC associates with DNA polymerase epsilon, via an evolutionarily conserved ‘Pol ϵ binding module’ in Ctf18-RFC that is produced by interaction of the carboxyl terminus of Ctf18 with the Ctf8 and Dcc1 subunits. Mutations at the end of Ctf18 disrupt the integrity of the Pol ϵ binding module and block the S-phase checkpoint pathway, downstream of the Mec1 kinase that is the budding yeast orthologue of mammalian ATR. Similar defects in checkpoint activation are produced by mutations that displace Pol ϵ from the replisome. These findings indicate that the association of Ctf18-RFC with Pol ϵ at defective replication forks is a key step in activation of the S-phase checkpoint. 相似文献
5.
Ausana Mapook Hiran A. Ariyawansa Saowaluck Tibpromma Erio Campesori E. B. Gareth Jones Ali H. Bahkali K. D. Hyde 《Mycological Progress》2016,15(4):34
Nodulosphaeria is a ubiquitous genus that comprises saprobic, endophytic and pathogenic species associated with a wide variety of substrates and has 64 species epithets listed in Index Fungorum. The classification of species in the genus has been a major challenge due to a lack of understanding of the importance of characters used to distinguish taxa, as well as the lack of reference strains. The present study clarifies the phylogenetic placement of the genus and related species, using fresh collections from Italy. Four Nodulosphaeria species are characterized based on multi-loci analyses of ITS, LSU, SSU, TEF and RPB2 sequence datasets. Phylogenetic analyses indicate that Nodulosphaeria species group within the family Phaeosphaeriaceae as a distinct genus. The sexual morphs of Nodulosphaeria hirta and N. spectabilis are described and illustrated using modern concepts. Two new Nodulosphaeria species are introduced. The phylogenetic relationships and taxonomy of the genus Nodulosphaeria are discussed, but further sampling with fresh collections, reference or ex-type strains and molecular data are needed to obtain a better and natural classification for the genus. 相似文献
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A K Yachou F Renaudie J L Guenet D Simon-Chazottes R Jones B Grandchamp C Beaumont 《Genomics》1991,10(3):531-538
Multiple ferritin H subunit sequences are present in the genome of higher vertebrates, but it is not yet known with certainty if more than one is expressed. In this paper, we provide evidence that there is only one functional ferritin H gene in the mouse. We screened a mouse genomic library using a mouse ferritin H cDNA as a probe and characterized five clones. These genomic clones proved to contain three pseudogenes and two allelic forms of a unique functional gene. These two alleles differed by only two point mutations in the promoter and three in the first intron and by a 31-bp insertion in the first intron. They were equally expressed when transiently transfected in HeLa cells. These five genomic clones account for all the bands observed on a Southern blot of mouse genomic DNA hybridized with a ferritin H cDNA, and these bands present a restriction fragment length polymorphism between various representatives of the genus Mus. Using a DNA panel prepared from the backcross progeny (C57BL/6 X Mus spretus)F1 X C57BL/6, we localized the functional ferritin H gene (Fth) in region B of mouse chromosome 19 and established cen-Ly-1-Fth-Pax-2 as the most likely gene order, thus defining a conserved syntenic fragment with human chromosome 11q. 相似文献
8.
H. Riad A. Nicholls J. Neuberger S. M. Willatts R. A. Sells M. A. Jones R. Francis 《BMJ (Clinical research ed.)》1995,310(6981):714-718
Elective ventilation describes the procedure of transferring selected patients dying from rapidly progressive intracranial haemorrhage from general medical wards to intensive care units for a brief period of ventilation before confirmation of brain stem death and harvesting of organs. This approach in Exeter has led to a rate of kidney retrieval and transplant higher than has been achieved elsewhere in the United Kingdom, with a stabilisation of numbers on patients on dialysis. Recently doubt has been cast on the legality of our practice of elective ventilation on the grounds that relatives are not permitted to consent to treatment of an incompetent person when that treatment is not in the patient''s best interests. We are thus faced with the dilemma of a protocol that is ethical, practical, and operates for the greater good but which may be illegal. This article explores various objections to the protocol and calls for public, medical, and legal debate on the issues. 相似文献
9.
Production,purification, and crystallization of human interleukin-1β converting enzyme derived from an Escherichia coli expression system 下载免费PDF全文
John J. Malinowski Bruce L. Grasberger Gary Trakshel Edward E. Huston Tracey M. Banks Patricia G. Brake Richard B. Ciccarelli Barry N. Jones James A. Koehn Diane Kratz Nicole Lundberg Panayiotis E. Stevis Carla T. Helaszek Mark A. Ator Angela M. Small Wood Travis Stams Byron Rubin Richard S. Alexander 《Protein science : a publication of the Protein Society》1995,4(10):2149-2155
10.
Florentina Negoita Julia Blomdahl Sebastian Wasserstrom Martin E. Winberg Peter Osmark Sara Larsson Karin G. Stenkula Mattias Ekstedt Stergios Kechagias Cecilia Holm Helena A. Jones 《Journal of cellular biochemistry》2019,120(1):343-356
The mechanism of how patatin-like phospholipase domain-containing protein 3 (PNPLA3) variant M148 is associated with increased risk of development of hepatic steatosis is still debated. Here, we propose a novel role of PNPLA3 as a key player during autophagosome formation in the process of lipophagy. A human hepatocyte cell line, HepG2 cells, expressing recombinant I148 or 148M, was used to study lipophagy under energy deprived conditions, and lipid droplet morphology was investigated using florescence microscopy, image analysis and biochemical assays. Autophagic flux was studied using the golden-standard of LC3-II turnover in combination with the well characterized GFP-RFP-LC3 vector. To discriminate between, perturbed autophagic initiation and lysosome functionality, lysosomes were characterized by Lysotracker staining and LAMP1 protein levels as well as activity and activation of cathepsin B. For validation, human liver biopsies genotyped for I148 and 148M were analyzed for the presence of LC3-II and PNPLA3 on lipid droplets. We show that the M148-PNPLA3 variant is associated with lipid droplets that are resistant to starvation-mediated degradation. M148 expressing hepatocytes reveal decreased autophagic flux and reduced lipophagy. Both I148-PNPLA3 and M148-PNPLA3 colocalize and interact with LC3-II, but the M148-PNPLA3 variant has lower ability to bind LC3-II. Together, our data indicate that PNPLA3 might play an essential role in lipophagy in hepatocytes and furthermore that the M148-PNPLA3 variant appears to display a loss in this activity, leading to decreased lipophagy. 相似文献