42 research outputs found
Ty1 integrase overexpression leads to integration of non-Ty1 DNA fragments into the genome of Saccharomyces cerevisiae
- Author
- A Galli
- AA Friedl
- AB Caumont
- Anna A. Friedl
- AT Bond
- CY Chan
- DJ Eichinger
- DJ Garfinkel
- EC Bolton
- EH Mules
- Friederike Eckardt-Schupp
- FX Wilhelm
- G Sharon
- GV Merkulov
- H Feldmann
- H Ji
- Horst G. Maxeiner
- J Horecka
- J Minic
- J Vera
- J Zhu
- JA Downs
- JA Downs
- JF Roth
- JM Kim
- K Tomita
- LT Braiterman
- M Frank-Vaillant
- M Kiechle
- M Kiechle
- M Koike
- M Wilhelm
- M Wilhelm
- MA Kenna
- Markus Kiechle
- N Bachman
- P Lesage
- P Manivasakam
- RD Gietz
- RD Gietz
- RH Schiestl
- RH Schiestl
- RH Schiestl
- Robert H. Schiestl
- SE Devine
- SE Lee
- SP Moore
- SP Moore
- SP Moore
- SP Moore
- V Lauermann
- V Parissi
- WY Yap
- Publication venue
- Springer-Verlag
- Publication date
- 01/01/2010
- Field of study
The integrase of the Saccharomyces cerevisiae retrotransposon Ty1 integrates Ty1 cDNA into genomic DNA likely via a transesterification reaction. Little is known about the mechanisms ensuring that integrase does not integrate non-Ty DNA fragments. In an effort to elucidate the conditions under which Ty1 integrase accepts non-Ty DNA as substrate, PCR fragments encompassing a selectable marker gene were transformed into yeast strains overexpressing Ty1 integrase. These fragments do not exhibit similarity to Ty1 cDNA except for the presence of the conserved terminal dinucleotide 5′-TG-CA-3′. The frequency of fragment insertion events increased upon integrase overexpression. Characterization of insertion events by genomic sequencing revealed that most insertion events exhibited clear hallmarks of integrase-mediated reactions, such as 5 bp target site duplication and target site preferences. Alteration of the terminal dinucleotide abolished the suitability of the PCR fragments to serve as substrates. We hypothesize that substrate specificity under normal conditions is mainly due to compartmentalization of integrase and Ty cDNA, which meet in virus-like particles. In contrast, recombinant integrase, which is not confined to virus-like particles, is able to accept non-Ty DNA, provided that it terminates in the proper dinucleotide sequence
Molecular characterization of HIV-1 genome in fission yeast Schizosaccharomyces pombe
- Author
- A Chino
- A Deora
- A Levin
- A Levin
- A Ono
- AB Caumont
- AD Hoffman
- AH Patki
- AW Cochrane
- BB Oude Essink
- C Zhang
- CD Weiss
- D Braaten
- D No
- DJ Kane
- DM Hockenbery
- DO Mitchison
- E Jacobs
- EO Freed
- EO Freed
- F Mammano
- F Stutz
- F Stutz
- G Basi
- G Li
- G Li
- GF Salgado
- HE Thomas
- HG Gottlinger
- J Sodroski
- JM McCune
- K Fineberg
- K Maundrell
- K Maundrell
- K Strebel
- K Takegawa
- L Fan
- L Herrero
- L Li
- LH Pearl
- M Braddock
- M Chen
- M Frei
- M Hardy
- M Hill
- M Lu
- M Piel
- M Suhasini
- M Thali
- MA Accola
- MA Ansari-Lari
- MH Malim
- MH Malim
- MJ Wichroski
- ML Andreola
- N Lewis
- NA Kootstra
- OK Haffar
- OT Fackler
- P Gallay
- Q Lu
- R Blanco
- R Toyama
- RH Dennin
- RT Elder
- RY Zhao
- S Huard
- S Iordanskiy
- SO Boe
- SS Carroll
- T Wilk
- TK Chiu
- U Schubert
- UK Schwedler von
- VW Pollard
- W Zhou
- Y Giga-Hama
- Y Yang
- Y Zhao
- Y Zhao
- Y Zhao
- Y Zhao
- Y Zhou
- Z Benko
- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- Field of study
Macrophages phagocytose nonopsonized silica particles using a unique microtubule-dependent pathway
- Author
- Aderem A
- Allen LA
- Bajno L
- Bartolini F
- Beamer CA
- Blackford JA
- Bohdanowicz M
- Caron E
- Caron E
- Castagna M
- Caumont AS
- Chao SK
- Costantini LM
- Cox D
- Cox D
- Daeron M
- Damen JE
- David A. Knecht
- Dent EW
- Desjardins M
- Duclos S
- Fitzer-Attas CJ
- Fubini B
- Ghazizadeh S
- Gilberti RM
- Gordon S
- Greenberg S
- Griffin FM
- Gu H
- Haberzettl P
- Hackam DJ
- Hall AB
- Hamilton R
- Hamilton RF
- Hanke JH
- Honda A
- Huaux F
- Indik Z
- Iyer R
- Iyer R
- Joshi GN
- Kiefer F
- Kobzik L
- Lee CY
- Lewkowicz E
- Loijens JC
- Machesky LM
- Marshall JG
- May RC
- May RC
- Newman SL
- Palecanda A
- Paul Forscher
- Pitt A
- Renée M. Gilberti
- Riedl J
- Scott CC
- Scott CC
- Shen HM
- Shi Y
- Stenmark H
- Suzuki T
- Swanson JA
- Taylor PR
- Thakur SA
- Thibodeau M
- Thibodeau MS
- Tjelle TE
- Toker A
- Vallyathan V
- Varnai P
- Vieira OV
- Vieira OV
- Vieira OV
- Yeung T
- Yvon AM
- Zhou J
- Zhou Q
- Publication venue
- 'American Society for Cell Biology (ASCB)'
- Publication date
- Field of study
Structural comparison of contractile nanomachines
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- Michel-Briand Y Baysse C
- Miyata ST Bachmann V, Pukatzki S
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- Robb CS Nano FE, Boraston AB
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- Ruska H
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- Publication venue
- 'American Institute of Mathematical Sciences (AIMS)'
- Publication date
- 01/01/2015
- Field of study
Determination of isotope ratio in the divertor of JET-ILW by high-resolution H alpha spectroscopy: H-D experiment and implications for D-T experiment
- Author
- Abduallev S
- Abhangi M
- Abreu P
- Afzal M
- Aggarwal KM
- Ahlgren T
- Ahn JH
- Aho-Mantila L
- Aiba N
- Airila M
- Albanese R
- Aldred V
- Alegre D
- Alessi E
- Aleynikov P
- Alfier A
- Alkseev A
- Allinson M
- Alper B
- Alves E
- Ambrosino G
- Ambrosino R
- Amicucci L
- Amosov V
- Angelone M
- Anghel M
- Angioni C
- Appel L
- Appelbee C
- Arena P
- Ariola M
- Arnichand H
- Arshad S
- Asakura NN
- Ash A
- Ashikawa N
- Aslanyan V
- Asunta O
- Auriemma F
- Austin Y
- Avotina L
- Axton MD
- Ayres C
- Bacharis M
- Baciero A
- Baiao D
- Bailey S
- Baker A
- Balboa I
- Balden M
- Balshaw N
- Bament R
- Banks JW
- Baranov YF
- Barnard MA
- Barnes D
- Barnes M
- Barnsley R
- Baruzzo M
- Basiuk V
- Bassan M
- Bastow R
- Batista A
- Batistoni P
- Baughan R
- Bauvir B
- Baylor L
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- Beal J
- Beaumont PS
- Beckers M
- Beckett B
- Becoulet A
- Bekris N
- Beldishevski M
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- Belli F
- Bellinger M
- Belonohy E
- Ben Ayed N
- Benterman NA
- Bergsaker H
- Bernardo J
- Bernert M
- Berry M
- Bertalot L
- Besliu C
- Beurskens M
- Bieg B
- Bielecki J
- Biewer T
- Bigi M
- Bilkova P
- Binda F
- Bisoffi A
- Bizarro JPS
- Bjorkas C
- Blackburn J
- Blackman K
- Blackman TR
- Blanchard P
- Blatchford P
- Bobkov V
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- Bodnar G
- Bogar O
- Bolshakova I
- Bolzonella T
- Bonanomi N
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- Zerbini M
- Zhang W
- Zhou Y
- Zilli E
- Zoita V
- Zoletnik S
- Zychor I
- Publication venue
- 'IOP Publishing'
- Publication date
- 01/01/2019
- Field of study
The data of the H alpha high-resolution spectroscopy, collected on the multiple lines of sight, which cover the entire divertor space in poloidal cross-section, during the recent hydrogen-deuterium experiments in JET-ILW (ITER-like wall), are processed. A strong spatial inhomogeneity of the hydrogen concentration, H/(H + D), in divertor is found in many pulses. Namely, the H/(H + D) ratio may be lower in the inner divertor than that in the outer divertor by the values of 0.15-0.35, depending on the conditions of gas puffing and plasma heating. This effect suggests the necessity of spatially-resolved measurements of isotope ratio in the divertor in the upcoming deuterium-tritium experiments. Also, separation of the overlapped T alpha and D alpha spectral lines is shown to be a challenging task especially when the local Doppler-broadened (Gaussian) line shapes are noticeably distorted by the net inward flux of fast non-Maxwellian neutral atoms. We use the respective, formerly developed model of an asymmetric spectral line shape, while analysing the data of the first deuterium-tritium experiment in JET-C (carbon wall), and test the model via comparing the isotope ratio results with another diagnostic's measurements. This model is shown to increase the accuracy of tritium concentration measurements in the divertor
Direct gyrokinetic comparison of pedestal transport in JET with carbon and ITER-like walls
- Author
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- Zychor I
- Publication venue
- 'IOP Publishing'
- Publication date
- 01/01/2019
- Field of study
This paper compares the gyrokinetic instabilities and transport in two representative JET pedestals, one (pulse 78697) from the JET configuration with a carbon wall (C) and another (pulse 92432) from after the installation of JET's ITER-like Wall (ILW). The discharges were selected for a comparison of JET-ILW and JET-C discharges with good confinement at high current (3 MA, corresponding also to low rho(*)) and retain the distinguishing features of JET-C and JET-ILW, notably, decreased pedestal top temperature for JET-ILW. A comparison of the profiles and heating power reveals a stark qualitative difference between the discharges: the JET-ILW pulse (92432) requires twice the heating power, at a gas rate of 1.9 x 10(22) e s(-1), to sustain roughly half the temperature gradient of the JET-C pulse (78697), operated at zero gas rate. This points to heat transport as a central component of the dynamics limiting the JET-ILW pedestal and reinforces the following emerging JET-ILW pedestal transport paradigm, which is proposed for further examination by both theory and experiment. ILW conditions modify the density pedestal in ways that decrease the normalized pedestal density gradient a/L-n, often via an outward shift in relation to the temperature pedestal. This is attributable to some combination of direct metal wall effects and the need for increased fueling to mitigate tungsten contamination. The modification to the density profile increases eta = L-n/L-T, thereby producing more robust ion temperature gradient (ITG) and electron temperature gradient driven instability. The decreased pedestal gradients for JET-ILW (92432) also result in a strongly reduced E x B shear rate, further enhancing the ion scale turbulence. Collectively, these effects limit the pedestal temperature and demand more heating power to achieve good pedestal performance. Our simulations, consistent with basic theoretical arguments, find higher ITG turbulence, stronger stiffness, and higher pedestal transport in the ILW plasma at lower rho(*)
Radial variation of heat transport in L-mode JET discharges
- Author
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- Publication venue
- 'IOP Publishing'
- Publication date
- 01/01/2019
- Field of study
In this paper, we analyze heat transport in the JET tokamak using data from its high resolution ECE diagnostic and analyses based on the transfer entropy (TE). The analysis reveals that heat transport is not smooth and continuous, but is characterized by 'trapping regions' separated by `minor transport barriers'. Meat may 'jump over' these barriers and when the heating power is raised, this 'jumping' behavior becomes more prominent. To check that our results are relevant for global heat transport, we deduced an effective diffusion coefficient from the TE results. Both its value and overall radial variation are consistent with heat diffusivities reported in literature. The detailed radial structure of the effective diffusion coefficient was shown to be linked to the mentioned minor transport barriers
EDGE2D-EIRENE simulations of the influence of isotope effects and anomalous transport coefficients on near scrape-off layer radial electric field
- Author
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- Publication venue
- 'IOP Publishing'
- Publication date
- 01/01/2019
- Field of study
EDGE2D-EIRENE (the 'code') simulations show that radial electric field, Er, in the near scrape-off layer (SOL) of tokamaks can have large variations leading to a strong local E x B shear greatly exceeding that in the core region. This was pointed out in simulations of JET plasmas with varying divertor geometry, where the magnetic configuration with larger predicted near SOL E-r was found to have lower H-mode power threshold, suggesting that turbulence suppression in the SOL by local E. x. B shear can be a player in the L-H transition physics (Delabie et al 2015 42nd EPS Conf. on Plasma Physics (Lisbon, Portugal, 22-26 June 2015) paper O3.113 (http://ocs.ciemat.es/EPS2015PAP/pdf/O3.113.pdf), Chankin et al 2017 Nucl. Mater. Energy 12 273). Further code modeling of JET plasmas by changing hydrogen isotopes (H-D-T) showed that the magnitude of the near SOL E-r is lower in H cases in which the H-mode threshold power is higher (Chankin et al 2017 Plasma Phys. Control. Fusion 59 045012). From the experiment it is also known that hydrogen plasmas have poorer particle and energy confinement than deuterium plasmas, consistent with the code simulation results showing larger particle diffusion coefficients at the plasma edge, including SOL, in hydrogen plasmas (Maggi et al 2018 Plasma Phys. Control. Fusion 60 014045). All these experimental observations and code results support the hypothesis that the near SOL E x B shear can have an impact on the plasma confinement. The present work analyzes neutral ionization patterns of JET plasmas with different hydrogen isotopes in L-mode cases with fixed input power and gas puffing rate, and its impact on target electron temperature, T-e, and SOL E-r. The possibility of a self-feeding mechanism for the increase in the SOL E-r via the interplay between poloidal E x B drift and target T-e is discussed. It is also shown that reducing anomalous turbulent transport coefficients, particle diffusion and electron and ion heat conductivities, leads to higher peak target T-e and larger E-r, suggesting the possibility of a positive feedback loop, under an implicitly made assumption that the E x B shear in the SOL is capable of suppressing turbulence
A power-balance model of the density limit in fusion plasmas: application to the L-mode tokamak
- Author
- Abduallev S
- Abhangi M
- Abreu P
- Afzal M
- Aggarwal KM
- Agostini FD
- Ahlgren T
- Ahn JH
- Aho-Mantila L
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- Alkseev A
- Allinson M
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- Ambrosino G
- Ambrosino R
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- Zerbini M
- Zhang W
- Zhou Y
- Zilli E
- Zoita V
- Zoletnik S
- Zychor I
- Publication venue
- 'IOP Publishing'
- Publication date
- 01/01/2019
- Field of study
A power-balance model, with radiation losses from impurities and neutrals, gives a unified description of the density limit (DL) of the stellarator, the L-mode tokamak, and the reversed field pinch (RFP). The model predicts a Sudo-like scaling for the stellarator, a Greenwald- like scaling, alpha I-p(8/9), for the RFP and the ohmic tokamak, a mixed scaling, alpha (PIp4/9)-I-4/9, for the additionally heated L-mode tokamak. In a previous paper (Zanca et al 2017 Nucl. Fusion 57 056010) the model was compared with ohmic tokamak, RFP and stellarator experiments. Here, we address the issue of the DL dependence on heating power in the L-mode tokamak. Experimental data from high-density disrupted L-mode discharges performed at JET, as well as in other machines, arc taken as a term of comparison. The model fits the observed maximum densities better than the pure Greenwald limit
Long-lived coupled peeling ballooning modes preceding ELMs on JET
- Author
- Abduallev S
- Abhangi M
- Abreu P
- Afzal M
- Aggarwal KM
- Agostini FD
- Ahlgren T
- Ahn JH
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- Publication venue
- 'IOP Publishing'
- Publication date
- 01/01/2019
- Field of study
In some JET discharges, type-I edge localised modes (ELMs) are preceded by a class of low-frequency oscillations (Perez et al 2004 Nucl. Fusion 44 609). While in many cases the ELM is triggered during the growth phase of this oscillation, it is also observed that this type of oscillation can saturate and last for several tens of ms until an ELM occurs. In order to identify the nature of these modes, a wide pre-ELM oscillation database, including detailed pedestal profile information, has been assembled and analysed in terms of MHD stability parameters. The existence domain of these pre-ELM oscillations and the statistical distribution of toroidal mode numbers (n) up to n = 16 have been mapped in ballooning alpha (alpha(ball)) and either edge current density (J(edge)) or pedestal collisionality (nu(ee,ped)*) coordinates and compared to linear MHD stability predictions. The pre-ELM oscillations are reliably observed when the J/alpha ratio is high enough for the pedestal to access the coupled peeling-ballooning (PB) domain (aka stability nose). Conversely, when the pedestal is found to be in or near the high-n ballooning domain (which is at low J/alpha ratio), ELMs are usually triggered promptly, i.e. with no detectable pre-ELM oscillations, or with pre-ELM oscillations only observable on ECE whose n appears to be too high to be resolved by the magnetics. Individual discharges can sometimes exhibit a fairly wide range of pre-ELM mode numbers, but for a wider database, the statistical n-number domains are found to be well ordered along the J - alpha stability boundary and behave as expected from PB theory: the higher the J/alpha ratio, the lower the mode's measured n tends to be. Within the measurement uncertainties, the measured n is usually found to be compatible with the most unstable n predicted by the linear stability code MISHKA1. These results confirm the earlier hypothesis that these modes are coupled peeling-ballooning modes, and extend and generalise to higher-mode numbers the work by Huysmans et al (1998 Nucl. Fusion 38 179), who identified the lowest n modes as pure external kink modes. Since the destabilisation of PB modes is widely accepted to give rise to ELMs, the mode saturation and delayed ELM triggering that is sometimes observed is rather unexpected. Possibilities to reconcile the extended lifetime of these modes with current ELM models are briefly discussed, but will require further investigation