bluuebunny/crossref_metadata_2025_split huggingface dataset:
A brute force postgenome approach to identify temperature‐sensitive mutations that negatively interact with separase and securin plasmids
Authors: Matsumura Takuhiro , Yuasa Tatsuro , Hayashi Takeshi , Obara Takayuki , Kimata Yuu , Yanagida Mitsuhiro 
Published: December 2004

AbstractBackground: The fission yeast Schizosaccharomyces pombe separase/Cut1 and securin/Cut2 are required for anaphase‐specific activation of proteolysis that leads to proper sister chromatid separation. We intended to identify ts (temperature sensitive) strains whose growth was inhibited by multicopy plasmid pCUT1 or pCUT2 at the permissive temperature.Results: After a one‐by‐one transformation of 1015 randomly isolated ts strains, 18 transformants that retarded in colony formation at the permissive or semipermissive temperature were isolated. Six of them, in the absence of pCUT1 or pCUT2, produced mitotic phenotypes with condensed chromosomes at the restrictive temperature. Gene cloning established that these mutants were defective in either the subunits (Cut9, Cut23, Cut20 or Apc10) of APC (anaphase promoting complex)/cyclosome or Cut8, a regulator for 26S proteasome localization. The inhibitory effect of separase against APC/cyclosome mutations was abolished when the catalytic site mutation C1730A was introduced and overproduced, indicating that inhibition needs an active separase. Securin/Cut2 overproduction also caused a negative effect on these mutants. Surprisingly, the phenotypes of cut9 and cut23 in the presence of pCUT1 or pCUT2 were not the mitotic arrest, and they were strikingly different depending on pCUT1 or pCUT2.Conclusions: This study shows the functional link between separase/Cut1 and APC/cyclosome in a separase activity‐dependent manner. The negative effect of active separase overproduction on APC/cyclosome mutations is possibly due to the direct inhibition of APC/cyclosome. In addition, the manner of the inhibition by high copy securin and separase plasmids were quite different each other and did not result in the mitotic block.
The small GTPase Rho4 is involved in controlling cell morphology and septation in fission yeast
Authors: Nakano Kentaro , Mutoh Tadashi , Arai Ritsuko , Mabuchi Issei 
Published: December 2004

AbstractBackground:Rho family small GTPases have been shown to be involved in various cellular activities, including the organization of actin cytoskeleton in eukaryotic cells. There are sixrhogenes in the fission yeastSchizosaccharomyces pombe. Cdc42 is known to control the polarity of the cell. Rho1, Rho2 and Rho3 play important roles in controlling cell shape and septation. On the other hand, Rho4 and Rho5 have not yet been characterized. Here we report the function ofrho4+in fission yeast.Results:Gene disruption revealed thatrho4+is not essential for cell growth. However,rho4‐null cells were abnormally elongated and had multiple septa of irregular shape at 37 °C. In these cells, F‐actin patches were randomly localized all over the cell periphery, and cytoplasmic microtubules (MTs) were misoriented. On the other hand, the exogenous expression of a constitutively active Rho4‐G23V or Rho4‐Q74L in wild‐type cells induced depolarization of F‐actin patches and cytoplasmic MTs. Rho4 was localized to the cell periphery during interphase and septum during mitosis. Both the binding of GTP and isoprenylation of its C‐terminus were necessary for the localization. Furthermore, the localization of Rho4 was likely to be controlled by Rho GAP and Rho GDI.Conclusion:Rho4 may control cell morphogenesis and septation by regulating both the actin cytoskeleton and cytoplasmic MTs.
Keap1 regulates both cytoplasmic‐nuclear shuttling and degradation of Nrf2 in response to electrophiles
Authors: Itoh Ken , Wakabayashi Nobunao , Katoh Yasutake , Ishii Tetsuro , O'Connor Tania , Yamamoto Masayuki 
Published: December 2004

AbstractBackground: Transcription factor Nrf2 regulates the expression of a set of detoxifying and anti‐oxidant enzyme genes. Several lines of evidence suggest that electrophiles and reactive oxygen species liberate Nrf2 from its cytoplasmic repressor Keap1 and provoke the accumulation of Nrf2 in the nucleus. To elucidate the molecular mechanisms as to how Nrf2 is activated by inducers, we examined the cytoplasmic‐nuclear shuttling and turnover of Nrf2.Results: We found that Nrf2 is rapidly degraded through the proteasome pathway, while electrophiles cause Nrf2 nuclear translocation with concomitant stabilization. Crucial to the inducible accumulation of Nrf2 is the enfeebling of the Nrf2–Keap1 interaction by electrophiles. Exploiting mice which have the LacZ reporter gene knocked into the nrf2 locus, we revealed that the inducible accumulation of Nrf2 protein by electrophiles in macrophages and intestinal epithelia could be recapitulated by the Nrf2 N‐terminal region in combination with a nuclear localization signal. We also found constitutive Nrf2 nuclear accumulation in Keap1‐deficient mouse macrophages.Conclusions: Our results highlight the fact that Nrf2 protein turnover is regulated by Keap1 mediated subcellular compartmentalization.
Caffeine mimics adenine and 2′‐deoxyadenosine, both of which inhibit the guanine‐nucleotide exchange activity of RCC1 and the kinase activity of ATR
Authors: Nishijima Hitoshi , Nishitani Hideo , Saito Noriko , Nishimoto Takeharu 
Published: December 2004

AbstractBackground: Both caffeine and the inactivation of RCC1, the guanine‐nucleotide exchange factor (GEF) of Ran, induce premature chromatin condensation (PCC) in hamster BHK21 cells arrested in the S‐phase, suggesting that RCC1 is a target for caffeine.Results: Caffeine inhibited the Ran‐GEF activity of RCC1 by preventing the binary complex formation of Ran‐RCC1. Inhibition of the Ran‐GEF activity of RCC1 by caffeine and its derivatives was correlated with their ability to induce PCC. Since caffeine is a derivative of xanthine, the bases and nucleosides were screened for their ability to inhibit RCC1. Adenine, adenosine, and all of the 2′‐deoxynucleosides inhibited the Ran‐GEF activity of RCC1; however, only adenine and 2′‐deoxyadenosine (2′‐dA) induced PCC. A factor(s) other than RCC1, should therefore be involved in PCC‐induction. We found that both adenine and 2′‐dA, but none of the other 2′‐deoxynucleosides, inhibited the kinase activity of ATR, similar to that of caffeine. The ATR pathway was also abrogated by the inactivation of RCC1 in tsBN2 cells.Conclusion: The effect of caffeine on cell‐cycle control mimics the biological effect of adenine and 2′‐dA, both of which inhibit ATR. dATP, a final metabolite of adenine and 2′‐dA, is suggested to inhibit ATR, resulting in PCC.
Budding yeastmcm10/dna43mutant requires a novel repair pathway for viability
Authors: Araki Yoshio , Kawasaki Yasuo , Sasanuma Hiroyuki , Tye Bik K. , Sugino Akio 
Published: December 2004

AbstractBackground:MCM10is essential for the initiation of chromosomal DNA replication inSaccharomyces cerevisiae. Mcm10p functionally interacts with components of the pre‐replicative complex (Mcm2‐Mcm7 complex and origin recognition complex) as well as the pre‐initiation complex component (Cdc45p) suggesting that it may be a component of the pre‐RC as well as the pre‐IC. Two‐dimensional gel electrophoresis analysis showed that Mcm10p is required not only for the initiation of DNA synthesis at replication origins but also for the smooth passage of replication forks at origins. Genetic analysis showed thatMCM10interacts with components of the elongation machinery such as Polδ and Polɛ, suggesting that it may play a role in elongation replication.Results:We show that themcm10mutation causes replication fork pausing not only at potentially active origins but also at silent origins. We screened for mutations that are lethal in combination withmcm10‐1and obtained seven mutants namedslm1‐slm6forsyntheticallylethal withmcm10. These mutants comprised six complementation groups that can be divided into three classes. Class 1 includes genes that encode components of the pre‐RC and pre‐IC and are represented bySLM3,4and5which are allelic toMCM7,MCM2andCDC45, respectively. Class 2 includes genes involved in the processing of Okazaki fragments in lagging strand synthesis and is represented bySLM1, which is allelic toDNA2. Class 3 includes novel DNA repair genes represented bySLM2andSLM6.Conclusions:The viability of themcm10‐1mutant is dependent on a novel repair pathway that may participate either in resolving accumulated replication intermediates or the damage caused by blocked replication forks. These results are consistent with the hypothesis that Mcm10p is required for the passage of replication forks through obstacles such as those created by pre‐RCs assembled at active or inactive replication origins.
Cloning and characterization of mCRIP2, a mouse LIM‐only protein that interacts with PDZ domain IV of PTP‐BL
Authors: Van Ham Marco , Croes Huib , Schepens Jan , Fransen Jack , Wieringa Bé , Hendriks Wiljan 
Published: December 2004

Abstract Background: In the mouse submembranous protein tyrosine phosphatase PTP‐BL five PDZ domains are present in between the N‐terminal FERM domain, which directs the protein to the cell cortex, and the C‐terminal catalytic phosphatase domain. To understand more on the physical role of PTP‐BL in this microenvironment, we started to search for PTP‐BL PDZ domain‐interacting proteins.Results: Yeast two‐hybrid screening for PTP‐BL targets resulted in the identification of a novel mouse LIM‐only protein termed CRIP2 that is highly homologous to rat ESP1 and human CRP2 sequences. Mouse CRIP2 has a predicted molecular weight of 23 kD and consists of two LIM domains spaced by 68 amino acids. The fourth PDZ domain of PTP‐BL is responsible for the binding of CRIP2 protein. Both PTP‐BL and CRIP2 mRNAs display a wide, overlapping tissue distribution. Western blot analysis revealed a more restricted expression pattern for CRIP2 with high expression in lung, heart and brain. CRIP2 protein is localized at cell cortical, actin‐rich structures, which is concurrent with the subcellular localization of PTP‐BL.Conclusions: The observed characteristics of the LIM domain‐containing adaptor protein CRIP2 are consistent with a potential role of PTP‐BL in the dynamics of the cortical actin cytoskeleton.
Antioxidant function of a novel selenoprotein in Drosophila melanogaster
Authors: Morozova Nadya , Forry Erin P. , Shahid Elena , Zavacki Ann Marie , Harney John W. , Kraytsberg Yevgenya , Berry Marla J. 
Published: December 2004

AbstractBackground:  Insects appear to have diverged from both higher and lower organisms in their defense mechanisms against oxidative damage. They do not encode glutathione peroxidases or glutathione reductases, and their thioredoxin reductases exhibit distinct properties from those of higher and lower species. Nonetheless, appropriate balance of anti‐oxidants and pro‐oxidants, and protection from damaging reactive oxygen species are clearly crucial in insects for viability, normal functioning of signalling pathways and morphogenesis, and have been implicated in studies on longevity in flies and other organisms.Results:  Two novel selenoproteins, dselH and dselK, were recently identified in Drosophila melanogaster. We have used RNAi in D. melanogaster embryos and in Schneider S2 cells to inhibit expression of these proteins. We report that inhibition of either dselH or dselK expression significantly reduces viability in embryos. We further show that dselH silencing decreases total anti‐oxidant capacity in embryos and Schneider cells, and increases lipid peroxidation in cells. Conversely, transient expression of dselH in the cell line decreases lipid peroxidation, and reverses the toxic effects of a glutathione‐depleting drug. The latter correlates with sparing of glutathione levels.Conclusions:  These studies suggest that the well‐known role of selenoproteins in vertebrate anti‐oxidant defenses also extends to include invertebrates.
Characterization of dipping fractures in a transverselyisotropic background
Authors: Grechka V. , Tsvankin I. 
Published: December 2004

ABSTRACTAlthough it is believed that natural fracture sets predominantly have near‐vertical orientation, oblique stresses and some other mechanisms may tilt fractures away from the vertical. Here, we examine an effective medium produced by a single system of obliquely dipping rotationally invariant fractures embedded in a transversely isotropic with a vertical symmetry axis (VTI) background rock. This model is monoclinic with a vertical symmetry plane that coincides with the dip plane of the fractures.Multicomponent seismic data acquired over such a medium possess several distinct features that make it possible to estimate the fracture orientation. For example, the vertically propagating fast shear wave (and the fast converted PS‐wave) is typically polarized in the direction of the fracture strike. The normal‐moveout (NMO) ellipses of horizontal reflection events are co‐orientated with the dip and strike directions of the fractures, which provides an independent estimate of the fracture azimuth. However, the polarization vector of the slow shear wave at vertical incidence does not lie in the horizontal plane – an unusual phenomenon that can be used to evaluate fracture dip. Also, for oblique fractures the shear‐wave splitting coefficient at vertical incidence becomes dependent on fracture infill (saturation).A complete medium‐characterization procedure includes estimating the fracture compliances and orientation (dip and azimuth), as well as the Thomsen parameters of the VTI background. We demonstrate that both the fracture and background parameters can be obtained from multicomponent wide‐azimuth data using the vertical velocities and NMO ellipses of PP‐waves and two split SS‐waves (or the traveltimes of PS‐waves) reflected from horizontal interfaces. Numerical tests corroborate the accuracy and stability of the inversion algorithm based on the exact expressions for the vertical and NMO velocities.
Azimuth moveout correction for transversely isotropic media
Authors: Alkhalifah Tariq 
Published: December 2004

ABSTRACTThe azimuth moveout (AMO) operator in homogeneous transversely isotropic media with a vertical symmetry axis (VTI), as in isotropic media, has an overall skewed saddle shape. However, the AMO operator in anisotropic media is complicated; it includes, among other things, triplications at low angles. Even in weaker anisotropies, with the anisotropy parameter η= 0.1 (10% anisotropy), the AMO operator is considerably different from the isotropic operator, although free of triplications. The structure of the operator in VTI media (positive η) is stretched (has a wider aperture) compared with operators in isotropic media, with the amount of stretch being dependent on the strength of anisotropy. If the medium is both vertically inhomogeneous, i.e. the vertical velocity is a function of depth (v(z)), and anisotropic, which is a common combination in practical problems, the shape of the operator again differs from that for isotropic media. However, the difference in the AMO operator between the homogeneous and the v(z) cases, even for anisotropic media, is small. Stated simply, anisotropy influences the shape and aperture of the AMO operator far more than vertical inhomogeneity does.
2.5D modelling, inversion and angle migration in anisotropic elastic media
Authors: Foss Stig‐Kyrre , Ursin Bjørn 
Published: December 2004

ABSTRACT2.5D modelling approximates 3D wave propagation in the dip‐direction of a 2D geological model. Attention is restricted to raypaths for waves propagating in a plane. In this way, fast inversion or migration can be performed. For velocity analysis, this reduction of the problem is particularly useful.We review 2.5D modelling for Born volume scattering and Born–Helmholtz surface scattering. The amplitudes are corrected for 3D wave propagation, taking into account both in‐plane and out‐of‐plane geometrical spreading. We also derive some new inversion/migration results. An AVA‐compensated migration routine is presented that is simplified compared with earlier results. This formula can be used to create common‐image gathers for use in velocity analysis by studying the residual moveout. We also give a migration formula for the energy‐flux‐normalized plane‐wave reflection coefficient that models large contrast in the medium parameters not treated by the Born and the Born–Helmholtz equation results. All results are derived using the generalized Radon transform (GRT) directly in the natural coordinate system characterized by scattering angle and migration dip. Consequently, no Jacobians are needed in their calculation.Inversion and migration in an orthorhombic medium or a transversely isotropic (TI) medium with tilted symmetry axis are the lowest symmetries for practical purposes (symmetry axis is in the plane). We give an analysis, using derived methods, of the parameters for these two types of media used in velocity analysis, inversion and migration. The kinematics of the two media involve the same parameters, hence there is no distinction when carrying out velocity analysis. The in‐plane scattering coefficient, used in the inversion and migration, also depends on the same parameters for both media. The out‐of‐plane geometrical spreading, necessary for amplitude‐preserving computations, for the TI medium is dependent on the same parameters that govern in‐plane kinematics. For orthorhombic media, information on additional parameters is required that is not needed for in‐plane kinematics and the scattering coefficients.Resolution analysis of the scattering coefficient suggests that direct inversion by GRT yields unreliable parameter estimates. A more practical approach to inversion is amplitude‐preserving migration followed by AVA analysis.SYMBOLS AND NOTATIONA list of symbols and notation is given in Appendix D.
The importance of low atmospheric CO2 and fire in promoting the spread of grasslands and savannas
Authors: BOND W. J. , MIDGLEY G. F. , WOODWARD F. I. 
Published: December 2004

AbstractThe distribution and abundance of trees can be strongly affected by disturbance such as fire. In mixed tree/grass ecosystems, recurrent grass‐fuelled fires can strongly suppress tree saplings and therefore control tree dominance. We propose that changes in atmospheric [CO2] could influence tree cover in such metastable ecosystems by altering their postburn recovery rates relative to flammable herbaceous growth forms such as grasses. Slow sapling recovery rates at low [CO2] would favour the spread of grasses and a reduction of tree cover. To test the possible importance of [CO2]/fire interactions, we first used a Dynamic Global Vegetation Model (DGVM) to simulate biomass in grassy ecosystems in South Africa with and without fire. The results indicate that fire has a major effect under higher rainfall conditions suggesting an important role for fire/[CO2] interactions. We then used a demographic model of the effects of fire on mesic savanna trees to test the importance of grass/tree differences in postburn recovery rates. We adjusted grass and tree growth in the model according to the DGVM output of net primary production at different [CO2] relative to current conditions. The simulations predicted elimination of trees at [CO2] typical of the last glacial period (180 ppm) because tree growth rate is too slow (15 years) to grow to a fire‐proof size of ca. 3 m. Simulated grass growth would produce an adequate fuel load for a burn in only 2 years. Simulations of preindustrial [CO2] (270 ppm) predict occurrence of trees but at low densities. The greatest increase in trees occurs from preindustrial to current [CO2] (360 ppm). The simulations are consistent with palaeo‐records which indicate that trees disappeared from sites that are currently savannas in South Africa in the last glacial. Savanna trees reappeared in the Holocene. There has also been a large increase in trees over the last 50–100 years. We suggest that slow tree recovery after fire, rather than differential photosynthetic efficiencies in C3 and C4 plants, might have been the significant factor in the Late Tertiary spread of flammable grasslands under low [CO2] because open, high light environments would have been a prerequisite for the spread of C4 grasses. Our simulations suggest further that low [CO2] could have been a significant factor in the reduction of trees during glacial times, because of their slower regrowth after disturbance, with fire favouring the spread of grasses.
Microbial characteristics of soils on a latitudinal transect in Siberia
Authors: ŠANTRU˚CˇKOVÁ HANA , BIRD MICHAEL I. , KALASCHNIKOV YEVGENIY N. , GRUND MILAN , ELHOTTOVÁ DANA , ŠIMEK MILOSLAV , GRIGORYEV SERGEY , GLEIXNER GERD , ARNETH ALMUT , SCHULZE ERNST‐DETLEF , LLOYD JON 
Published: December 2004

AbstractSoil microbial properties were studied from localities on a transect along the Yenisei River, Central Siberia. The 1000 km‐long transect, from 56°N to 68°N, passed through tundra, taiga and pine forest characteristic of Northern Russia. Soil microbial properties were characterized by dehydrogenase activity, microbial biomass, composition of microbial community (PLFAs), respiration rates, denitrification and N mineralization rates. Relationships between vegetation, latitude, soil quality (pH, texture), soil organic carbon (SOC) and the microbial properties were examined using multivariate analysis. In addition, the temperature responses of microbial growth (net growth rate) and activity (soil respiration rate) were tested by laboratory experiments. The major conclusions of the study are as follows:1. Multivariate analysis of the data revealed significant differences in microbial activity. SOC clay content was positively related to clay content. Soil texture and SOC exhibited the dominant effect on soil microbial parameters, while the vegetation and climatic effects (expressed as a function of latitude) were weaker but still significant. The effect of vegetation cover is linked to SOC quality, which can control soil microbial activity.2. When compared to fine‐textured soils, coarse‐textured soils have (i) proportionally more SOC bound in microbial biomass, which might result in higher susceptibility of SOC transformation to fluctuation of environmental factors, and (ii) low mineralization potential, but with a substantial part of the consumed C being transformed to microbial products.3. The soil microbial community from the northernmost study region located within the permafrost zone appears to be adapted to cold conditions. As a result, microbial net growth rate became negative when temperature rose above 5 °C and C mineralization then exceeded C accumulation.
A new assessment of European forests carbon exchanges by eddy fluxes and artificial neural network spatialization
Authors: PAPALE DARIO , VALENTINI RICCARDO 
Published: December 2004

AbstractRecently flux tower data have become available for a variety of ecosystems under different climatic and edaphic conditions. Although Flux tower data represent point measurements with a footprint of typically 1 km × 1 km they can be used to validate models and to spatialize biospheric fluxes at regional and continental scales. In this paper we present a study where biospheric flux data collected in the EUROFLUX project were used to train a neural network simulator to provide spatial (1 km × 1 km) and temporal (weekly) estimates of carbon fluxes of European forests at continental scale. The novelty of the approach is that flux data were used to constrain and parameterize the neural network structure using a limited number of input driving variables. The overall European carbon uptake from this analysis was 0.47 Gt C yr−1with distinctive differences between boreal and temperate regions. The length of the growing season is longer in the south of Europe (about 32 weeks), compared with north and central Europe, which have a similar length‐growing season (about 27 weeks). A peak in respiration was depicted in spring at continental scale as a coherent signal which parallel the construction respiration increase at the onset of the season as usually shown by leaf level measurements.