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51.
Sergey N. Mikhailov Erik De Clercq Piet Herdewijn 《Nucleosides, nucleotides & nucleic acids》2013,32(7-8):1323-1334
Abstract The previously developed method for the preparation of 2′-O-D-ribofuranosyl-nucleosides is extended to ribosylation of 2′-deoxynucleosides. The scope and limitations of this reaction are discussed. 相似文献
52.
53.
Wei Su Sergey V. Slepenkov Michael K. Slevin Shawn M. Lyons Marcin Ziemniak Joanna Kowalska Edward Darzynkiewicz Jacek Jemielity William F. Marzluff Robert E. Rhoads 《RNA (New York, N.Y.)》2013,19(1):1-16
Metazoan replication-dependent histone mRNAs are only present in S-phase, due partly to changes in their stability. These mRNAs end in a unique stem–loop (SL) that is required for both translation and cell-cycle regulation. Previous studies showed that histone mRNA degradation occurs through both 5′→3′ and 3′→5′ processes, but the relative contributions are not known. The 3′ end of histone mRNA is oligouridylated during its degradation, although it is not known whether this is an essential step. We introduced firefly luciferase reporter mRNAs containing the histone 3′ UTR SL (Luc-SL) and either a normal or hDcp2-resistant cap into S-phase HeLa cells. Both mRNAs were translated, and translation initially protected the mRNAs from degradation, but there was a lag of ∼40 min with the uncleavable cap compared to ∼8 min for the normal cap before rapid decay. Knockdown of hDcp2 resulted in a similar longer lag for Luc-SL containing a normal cap, indicating that 5′→3′ decay is important in this system. Inhibition of DNA replication with hydroxyurea accelerated the degradation of Luc-SL. Knockdown of terminal uridyltransferase (TUTase) 4 but not TUTase 3 slowed the decay process, but TUTase 4 knockdown had no effect on destabilization of the mRNA by hydroxyurea. Both Luc-SL and its 5′ decay intermediates were oligouridylated. Preventing oligouridylation by 3′-deoxyadenosine (cordycepin) addition to the mRNA slowed degradation, in the presence or absence of hydroxyurea, suggesting oligouridylation initiates degradation. The spectrum of oligouridylated fragments suggests the 3′→5′ degradation machinery stalls during initial degradation, whereupon reuridylation occurs. 相似文献
54.
Raeid M. M. Abed Sergey Dobretsov Marwan Al-Fori Sarath P. Gunasekera Kumar Sudesh Valerie J. Paul 《Journal of industrial microbiology & biotechnology》2013,40(7):759-772
In this study, extremely halophilic and moderately thermophilic microorganisms from a hypersaline microbial mat were screened for their ability to produce antibacterial, antidiatom, antialgal, and quorum-sensing (QS) inhibitory compounds. Five bacterial strains belonging to the genera Marinobacter and Halomonas and one archaeal strain belonging to the genus Haloterrigena were isolated from a microbial mat. The strains were able to grow at a maximum salinity of 22–25 % and a maximum temperature of 45–60 °C. Hexanes, dichloromethane, and butanol extracts from the strains inhibited the growth of at least one out of nine human pathogens. Only butanol extracts of supernatants of Halomonas sp. SK-1 inhibited growth of the microalga Dunaliella salina. Most extracts from isolates inhibited QS of the acyl homoserine lactone producer and reporter Chromobacterium violaceum CV017. Purification of QS inhibitory dichloromethane extracts of Marinobacter sp. SK-3 resulted in isolation of four related diketopiperazines (DKPs): cyclo(l-Pro-l-Phe), cyclo(l-Pro-l-Leu), cyclo(l-Pro-l-isoLeu), and cyclo(l-Pro-d-Phe). QS inhibitory properties of these DKPs were tested using C. violaceum CV017 and Escherichia coli-based QS reporters (pSB401 and pSB1075) deficient in AHL production. Cyclo(l-Pro-l-Phe) and cyclo(l-Pro-l-isoLeu) inhibited QS-dependent production of violacein by C. violaceum CV017. Cyclo(l-Pro-l-Phe), cyclo(l-Pro-l-Leu), and cyclo(l-Pro-l-isoLeu) reduced QS-dependent luminescence of the reporter E. coli pSB401 induced by 3-oxo-C6-HSL. Our study demonstrated the ability of halophilic and moderately thermophilic strains from a hypersaline microbial mat to produce biotechnologically relevant compounds that could be used as antifouling agents. 相似文献
55.
Todd J Treangen Sergey Koren Daniel D Sommer Bo Liu Irina Astrovskaya Brian Ondov Aaron E Darling Adam M Phillippy Mihai Pop 《Genome biology》2013,14(1):R2
We describe MetAMOS, an open source and modular metagenomic assembly and analysis pipeline. MetAMOS represents an important step towards fully automated metagenomic analysis, starting with next-generation sequencing reads and producing genomic scaffolds, open-reading frames and taxonomic or functional annotations. MetAMOS can aid in reducing assembly errors, commonly encountered when assembling metagenomic samples, and improves taxonomic assignment accuracy while also reducing computational cost. MetAMOS can be downloaded from: https://github.com/treangen/MetAMOS. 相似文献
56.
Svetlana V. Kostyuk Marina S. Konkova Elizaveta S. Ershova Anna J. Alekseeva Tatiana D. Smirnova Sergey V. Stukalov Ekaterina A. Kozhina Nadezda V. Shilova Tatiana V. Zolotukhina Zhanna G. Markova Vera L. Izhevskaya Ancha Baranova Natalia N. Veiko 《PloS one》2013,8(10)
Background
Cell free DNA (cfDNA) circulates throughout the bloodstream of both healthy people and patients with various diseases and acts upon the cells. Response to cfDNA depends on concentrations and levels of the damage within cfDNA. Oxidized extracellular DNA acts as a stress signal and elicits an adaptive response.Principal Findings
Here we show that oxidized extracellular DNA stimulates the survival of MCF-7 tumor cells. Importantly, in cells exposed to oxidized DNA, the suppression of cell death is accompanied by an increase in the markers of genome instability. Short-term exposure to oxidized DNA results in both single- and double strand DNA breaks. Longer treatments evoke a compensatory response that leads to a decrease in the levels of chromatin fragmentations across cell populations. Exposure to oxidized DNA leads to a decrease in the activity of NRF2 and an increase in the activity of NF-kB and STAT3. A model that describes the role of oxidized DNA released from apoptotic cells in tumor biology is proposed.Conclusions/Significance
Survival of cells with an unstable genome may substantially augment progression of malignancy. Further studies of the effects of extracellular DNA on malignant and normal cells are warranted. 相似文献57.
Sergey M. Abramov Elmira R. Sadraddinova Andrey I. Shestakov Oleg G. Voronin Arkadiy A. Karyakin Nikolay A. Zorin Alexander I. Netrusov 《PloS one》2013,8(11)
Hydrogen-producing thermophilic cellulolytic microorganisms were isolated from cow faeces. Rates of cellulose hydrolysis and hydrogen formation were 0.2 mM L-1 h-1 and 1 mM L-1 h-1, respectively. An enzymatic fuel cell (EFC) with a hydrogenase anode was used to oxidise hydrogen produced in a microbial bioreactor. The hydrogenase electrode was exposed for 38 days (912 h) to a thermophilic fermentation medium. The hydrogenase activity remaining after continuous operation under load was 73% of the initial value. 相似文献
58.
Excitation of surface plasmons in metallic nanoparticles is a promising method for increasing the light absorption in solar cells and hence the cell photocurrent. Comprehensive optimization of a nanoparticle fabrication process for enhanced performance of polycrystalline silicon thin-film solar cells is presented. Three factors were studied: the Ag precursor film thickness, annealing temperature and time. The thickness of the precursor film was 10, 14 and 20 nm; annealing temperature was 190, 200, 230 and 260 °C; and annealing time was varied between 20 and 95 min. Performance enhancement due to light-scattering by nanoparticles was calculated by comparing absorption, short-circuit current density and energy conversion efficiency in solar cells with and without nanoparticles formed under different process conditions. Nanoparticles formed from 14-nm-thick Ag precursor film annealed at 230 °C for 53 min result in the highest absorption enhancement in the 700–1,100 nm wavelength range, in the highest enhancement of total short-circuit current density. The highest photocurrent enhancement was 33.5 %, which was achieved by the cell with the highest absorption enhancement in the 700–1,100 nm range. The plasmonic cell efficiency of 5.32 % was achieved without a back reflector and 5.95 % with the back reflector; which is the highest reported efficiency for plasmonic thin-film solar cells. 相似文献
59.
Jing Rao Sergey Varlamov Jongsung Park Svetlana Dligatch Anatoli Chtanov 《Plasmonics (Norwell, Mass.)》2013,8(2):785-791
Surface plasmonic-enhanced light trapping from metal nanoparticles is a promising way of increasing the light absorption in the active silicon layer and, therefore, the photocurrent of the silicon solar cells. In this paper, we applied silver nanoparticles on the rear side of polycrystalline silicon thin film solar cell and systematically studied the dielectric environment effect on the absorption and short-circuit current density (Jsc) of the device. Three different dielectric layers, magnesium fluoride (MgF2, n?=?1.4), tantalum pentoxide (Ta2O5, n?=?2.2), and titanium dioxide (TiO2, n?=?2.6), were investigated. Experimentally, we found that higher refractive index dielectric coatings results in a redshift of the main plasmonic extinction peak and higher modes were excited within the spectral region that is of interest in our thin film solar cell application. The optical characterization shows that nanoparticles coated with highest refractive index dielectric TiO2 provides highest absorption enhancement 75.6 %; however, from the external quantum efficiency characterization, highest short-circuit current density Jsc enhancement of 45.8 % was achieved by coating the nanoparticles with lower refractive index MgF2. We also further optimize the thickness of MgF2 and a final 50.2 % Jsc enhancement was achieved with a 210-nm MgF2 coating and a back reflector. 相似文献
60.
Alexandra M. Lopes Kenneth I. Aston Emma Thompson Filipa Carvalho Jo?o Gon?alves Ni Huang Rune Matthiesen Michiel J. Noordam Inés Quintela Avinash Ramu Catarina Seabra Amy B. Wilfert Juncheng Dai Jonathan M. Downie Susana Fernandes Xuejiang Guo Jiahao Sha António Amorim Alberto Barros Angel Carracedo Zhibin Hu Matthew E. Hurles Sergey Moskovtsev Carole Ober Darius A. Paduch Joshua D. Schiffman Peter N. Schlegel Mário Sousa Douglas T. Carrell Donald F. Conrad 《PLoS genetics》2013,9(3)
Gonadal failure, along with early pregnancy loss and perinatal death, may be an important filter that limits the propagation of harmful mutations in the human population. We hypothesized that men with spermatogenic impairment, a disease with unknown genetic architecture and a common cause of male infertility, are enriched for rare deleterious mutations compared to men with normal spermatogenesis. After assaying genomewide SNPs and CNVs in 323 Caucasian men with idiopathic spermatogenic impairment and more than 1,100 controls, we estimate that each rare autosomal deletion detected in our study multiplicatively changes a man''s risk of disease by 10% (OR 1.10 [1.04–1.16], p<2×10−3), rare X-linked CNVs by 29%, (OR 1.29 [1.11–1.50], p<1×10−3), and rare Y-linked duplications by 88% (OR 1.88 [1.13–3.13], p<0.03). By contrasting the properties of our case-specific CNVs with those of CNV callsets from cases of autism, schizophrenia, bipolar disorder, and intellectual disability, we propose that the CNV burden in spermatogenic impairment is distinct from the burden of large, dominant mutations described for neurodevelopmental disorders. We identified two patients with deletions of DMRT1, a gene on chromosome 9p24.3 orthologous to the putative sex determination locus of the avian ZW chromosome system. In an independent sample of Han Chinese men, we identified 3 more DMRT1 deletions in 979 cases of idiopathic azoospermia and none in 1,734 controls, and found none in an additional 4,519 controls from public databases. The combined results indicate that DMRT1 loss-of-function mutations are a risk factor and potential genetic cause of human spermatogenic failure (frequency of 0.38% in 1306 cases and 0% in 7,754 controls, p = 6.2×10−5). Our study identifies other recurrent CNVs as potential causes of idiopathic azoospermia and generates hypotheses for directing future studies on the genetic basis of male infertility and IVF outcomes. 相似文献