bluuebunny/crossref_metadata_2025 huggingface dataset:
An eddy‐permitting, dynamically consistent adjoint‐based assimilation system for the tropical Pacific: Hindcast experiments in 2000
Authors: Hoteit I. , Cornuelle B. , Heimbach P.
Published: March 2010

An eddy‐permitting adjoint‐based assimilation system has been implemented to estimate the state of the tropical Pacific Ocean. The system uses the Massachusetts Institute of Technology's general circulation model and its adjoint. The adjoint method is used to adjust the model to observations by controlling the initial temperature and salinity; temperature, salinity, and horizontal velocities at the open boundaries; and surface fluxes of momentum, heat, and freshwater. The model is constrained with most of the available data sets in the tropical Pacific, including Tropical Atmosphere and Ocean, ARGO, expendable bathythermograph, and satellite SST and sea surface height data, and climatologies. Results of hindcast experiments in 2000 suggest that the iterated adjoint‐based descent is able to significantly improve the model consistency with the multivariate data sets, providing a dynamically consistent realization of the tropical Pacific circulation that generally matches the observations to within specified errors. The estimated model state is evaluated both by comparisons with observations and by checking the controls, the momentum balances, and the representation of small‐scale features that were not well sampled by the observations used in the assimilation. As part of these checks, the estimated controls are smoothed and applied in independent model runs to check that small changes in the controls do not greatly change the model hindcast. This is a simple ensemble‐based uncertainty analysis. In addition, the original and smoothed controls are applied to a version of the model with doubled horizontal resolution resulting in a broadly similar “downscaled” hindcast, showing that the adjustments are not tuned to a single configuration (meaning resolution, topography, and parameter settings). The time‐evolving model state and the adjusted controls should be useful for analysis or to supply the forcing, initial, and boundary conditions for runs of other models.
Data‐based estimation of anthropogenic carbon and acidification in the Weddell Sea on a decadal timescale
Authors: Hauck J. , Hoppema M. , Bellerby R. G. J. , Völker C. , Wolf‐Gladrow D.
Published: March 2010

The amount of anthropogenic CO2 (Cant) that entered the Weddell Sea between 1992 and 2008 (Cant1992–2008) was assessed using the extended multiple linear regression (eMLR) method. In the Warm Deep Water (WDW) and the Weddell Sea Bottom Water (WSBW), Cant1992–2008 values were insignificant, whereas values as high as 8 μmol kg−1 were observed over the shelf. Cant1992–2008 concentrations in the surface layer varied with latitude between 2 and 11 μmol kg−1. Weak intrusion of anthropogenic CO2 into Weddell Sea Deep Water (WSDW) was demonstrated (Cant1992–2008 yields 1.5–2 μmol kg−1). That more Cant1992–2008 was found in the WSDW than in the WSBW is surprising, but can be explained by intense ventilation of the WSDW originating from east of the Weddell Gyre. The invasion of Cant1992–2008 provokes a shift in the equilibria of the carbonate system, resulting in acidification and reduction of CO32− concentration. The mean decrease of pH in the upper 200 m layer was 0.016. The largest decrease of calcite and aragonite saturation states was observed at the surface. This implies that surface waters might become undersaturated with respect to aragonite in the future while the underlying WDW is still saturated. Results of this analysis suggest that complete undersaturation of surface waters in the Weddell Sea will be reached after the 21st century.
Harnessing Aquatic Yeasts For Developing A New Generation of Sunscreens
Authors: Braganca Hycienth , Kamat Nandkumar
Published: March 2010

Around 100 yeast genera and 800 species have been isolated and characterized. Nagahama (2006) has reviewed yeast biodiversity in freshwater, marine and deep-Sea Environments. Our work aims at systematic biodiversity assessment of freshwater aquatic yeasts from Goa with major focus on carotenogenic basidiomycetes yeasts which on exposure to potentially damaging levels of solar ultraviolet radiation (UVR) accumulate photoprotective compounds (PPC) such as mycosporine-glutaminol-glucoside (myc-glu-glu, peak absorption at 309-310nm) that server as sunscreens and /or antioxidant. These yeasts are a potential source of a particularly diverse family of such substances, collectively referred to as mycosporine- like amino-acids (MAAs). This paper presents the potential of exploiting MAAs to develop a new generation of ecofriendly sunscreens.
The TA-p73 functions as a Lung tumor suppressor by increasing the expression of miRNA, let-7
Authors: Boominathan Lakshmanane
Published: March 2010

I have previously proposed that TA-p73-depenedent tumor suppressor pathway could inhibit the development of lung adenocarcinoma. This hypothesis is strongly supported by a recent finding showing that TA-p73 specific knockout mice are prone to lung adenocarcinoma. However, the p73-dependent tumor suppressor pathway remains ill defined. It has been shown that let-7 cluster is highly expressed in normal lung. Loss of let-7 expression: a) is common in Non-small cell lung carcinoma; and b) enhances lung tumor formation, indicating that it could function as a lung tumor suppressor. Based on these facts, I hypothesized that let-7 could be a transcriptional target of p73. To confirm this hypothesis, I have analyzed the let-7 cluster promoters using TRASFAC bioinformatics software. This analysis suggests that Let-7c contains three perfect p53-RE half-sites and five nearly perfect p53RE sites. In addition, other let-7 cluster miRNAs appear to contain several p53-REs, suggesting that Let-7 miRNA cluster could be a transcriptional target of p73/p63/p53. Furthermore, negative regulators of let-7 biogenesis, such as lin-28, c-myc and DCAMKL-1, are suppressed by p53-miRs, such as let-7, miR-145, miR-34, miR-15/16, miR-103/107 and miR-221, suggesting that TA-p73/p63/p53, by suppressing the expression of lin-28, c-myc and DCAMKL-1, it could increase the expression of let-7. By increasing the expression of let-7, TA-p73 could suppress the expression of its targets, such as N/H/K-ras, HMGA2, Cyclins, MCMs, BUBs, and CDCs; thereby it could inhibit the initiation of lung tumors. Together, this study proposes for the first time the TA-p73/p63-let-7-INK4a/ARF as a lung tumor suppressor pathway.
The umbilical cord matrix is a better source of mesenchymal stem cells (MSC) than the umbilical cord blood
Authors: Zeddou Mustapha , Briquet Alexandra , Relic Biserka , Josse Claire , Malaise Michel G. , Gothot André , Lechanteur Chantal , Beguin Yves
Published: March 2010

Many studies have drawn attention to the emerging role of MSC (mesenchymal stem cells) as a promising population supporting new clinical concepts in cellular therapy. However, the sources from which these cells can be isolated are still under discussion. Whereas BM (bone marrow) is presented as the main source of MSC, despite the invasive procedure related to this source, the possibility of isolating sufficient numbers of these cells from UCB (umbilical cord blood) remains controversial. Here, we present the results of experiments aimed at isolating MSC from UCB, BM and UCM (umbilical cord matrix) using different methods of isolation and various culture media that summarize the main procedures and criteria reported in the literature. Whereas isolation of MSC were successful from BM (10:10) and (UCM) (8:8), only one cord blood sample (1:15) gave rise to MSC using various culture media [DMEM (Dulbecco's modified Eagle's medium) +5% platelet lysate, DMEM+10% FBS (fetal bovine serum), DMEM+10% human UCB serum, MSCGM®] and different isolation methods [plastic adherence of total MNC (mononuclear cells), CD3+/CD19+/CD14+/CD38+‐depleted MNC and CD133+‐ or LNGFR+‐enriched MNC]. MSC from UCM and BM were able to differentiate into adipocytes, osteocytes and hepatocytes. The expansion potential was highest for MSC from UCM. The two cell populations had CD90+/CD73+/CD105+ phenotype with the additional expression of SSEA4 and LNGFR for BM MSC. These results clearly exclude UCB from the list of MSC sources for clinical use and propose instead UCM as a rich, non‐invasive and abundant source of MSC.
Comparative NMR studies of diffusional water permeability of red blood cells from different species: XVIII platypus (Ornithorhynchus anatinus) and saltwater crocodile (Crocodylus porosus)
Authors: Benga Gheorghe , Chapman Bogdan E. , Cox Guy C. , Kuchel Philip W.
Published: March 2010

As part of a programme of comparative measurements of P d (diffusional water permeability) the RBCs (red blood cells) from an aquatic monotreme, platypus (Ornithorhynchus anatinus), and an aquatic reptile, saltwater crocodile (Crocodylus porosus) were studied. The mean diameter of platypus RBCs was estimated by light microscopy and found to be ∼6.3 μm. P d was measured by using an Mn2+‐doping 1H NMR (nuclear magnetic resonance) technique. The P d (cm/s) values were relatively low: ∼2.1×10−3 at 25°C, 2.5×10−3 at 30°C, 3.4×10−3 at 37°C and 4.5 at 42°C for the platypus RBCs and ∼2.8×10−3 at 25°C, 3.2×10−3 at 30°C, 4.5×10−3 at 37°C and 5.7×10−3 at 42°C for the crocodile RBCs. In parallel with the low water permeability, the E a,d (activation energy of water diffusion) was relatively high, ∼35 kJ/mol. These results suggest that “conventional” WCPs (water channel proteins), or AQPs (aquaporins), are probably absent from the plasma membranes of RBCs from both the platypus and the saltwater crocodile.
Influence of traps on transient electric field and mobility evaluation in organic field-effect transistors
Authors: Manaka Takaaki , Liu Fei , Weis Martin , Iwamoto Mitsumasa
Published: March 2010

A significant difference between the transient electric field profiles of the pentacene organic field-effect transistors (OFETs) with SiO2 and poly(methyl-methacrylate) (PMMA) insulators was found by the time-resolved microscopic optical second-harmonic generation (TRM-SHG) experiment. The profile of former device was broad and changed smoothly, while the latter one had a sharp peak. Particularly, the peak of the transient electric field in SiO2-insulated devices moved much faster than that in the PMMA-insulated one. Based on several experimental evidences and computational simulations, we proposed that these differences might arise from a higher trapped carrier density in the conductive channel on the PMMA insulator. Simple approaches were developed to evaluate the trap density and define dynamic carrier mobility in terms of the transient electric field measured by the TRM-SHG technique. This mobility quantitatively depicts that the transient hole transport in the OFET with the PMMA insulator is trap controlled.
Comment on “On tractability of path integration” [J. Math. Phys. 37, 2071 (1996)]
Authors: Zhang Shun
Published: March 2010

We correct an omission in the proof of Theorem 3 in this paper.
Rate equations analysis of external-cavity quantum cascade lasers
Authors: Yang Q. K. , Hinkov B. , Fuchs F. , Bronner W. , Köhler K. , Wagner J. , Maulini R. , Faist J.
Published: March 2010

We present a comprehensive analysis of an external-cavity (EC) quantum cascade (QC) laser system, which is based on a coupled-mode system with the length of the EC set equal to that of the laser chip and accommodating the large difference in physical cavity length by introducing an effective speed of light for light propagating in the EC. By analyzing the rate equations and discussing the cross sections and losses of the EC QC lasers, numerical results as well as suggestions for a further optimization of the spectral tuning range of the EC system are presented. Besides, the delayed onset of the EC modes with respect to that of the internal Fabry–Perot modes in pulsed operation has been simulated using the rate equations, yielding a good agreement with the experimental data.
Structural investigations and magnetic properties of sol-gel Ni0.5Zn0.5Fe2O4 thin films for microwave heating
Authors: Gao Pengzhao , Rebrov Evgeny V. , Verhoeven Tiny M. W. G. M. , Schouten Jaap C. , Kleismit Richard , Kozlowski Gregory , Cetnar John , Turgut Zafer , Subramanyam Guru
Published: March 2010

Nanocrystalline Ni0.5Zn0.5Fe2O4 thin films have been synthesized with various grain sizes by a sol-gel method on polycrystalline silicon substrates. The morphology, magnetic, and microwave absorption properties of the films calcined in the 673–1073 K range were studied with x-ray diffraction, scanning electron microscopy, x-ray photoelectron spectroscopy, atomic force microscopy, vibrating sample magnetometry, and evanescent microwave microscopy. All films were uniform without microcracks. Increasing the calcination temperature from 873 to 1073 K and time from 1 to 3 h resulted in an increase of the grain size from 12 to 27 nm. The saturation and remnant magnetization increased with increasing the grain size, while the coercivity demonstrated a maximum near a critical grain size of 21 nm due to the transition from monodomain to multidomain behavior. The complex permittivity of the Ni–Zn ferrite films was measured in the frequency range of 2–15 GHz. The heating behavior was studied in a multimode microwave cavity at 2.4 GHz. The highest microwave heating rate in the temperature range of 315–355 K was observed in the film close to the critical grain size.
Effects of symmetry and Stone–Wales defect on spin-dependent electronic transport in zigzag graphene nanoribbons
Authors: Ren Yun , Chen Ke-Qiu
Published: March 2010

Spin-dependent electronic transport properties in zigzag graphene nanoribbons (ZGNRs) are studied using first-principles quantum transport calculations. The effects of the symmetry and defect have been considered. The results show that when the spin polarization is considered, both symmetric and asymmetric ZGNRs present semiconductor behavior, which is different from spin-unpolarized result. The symmetry of ZGNRs plays an important role in electron transport behavior. Asymmetric ZGNR displays monotonic transport behavior. However, in symmetric ZGNRs systems, negative differential resistance is observed. The influence of defect is more obvious in symmetric ZGNRs than in asymmetric systems. A physical analysis of these results is given.
Model for the description of ion beam extraction from electron cyclotron resonance ion sources
Authors: Spädtke P.
Published: March 2010

The finite difference method trajectory code KOBRA3-INP has been developed now for 25 years to perform the simulation of ion beam extraction in three dimensions. Meanwhile, the code has been validated for different applications: high current ion beam extraction from plasma sources for ion implantation technology, neutral gas heating in fusion devices, or ion thrusters for space propulsion. One major issue of the development of this code was to improve the flexibility of the applied model for the simulation of different types of particle sources. Fixed emitter sources might be simulated with that code as well as laser ion sources, Penning ion sources, electron cyclotron resonance ion sources (ECRISs), or H− sources, which require the simulation of negative ions, negative electrons, and positive charges simultaneously. The model which has been developed for ECRIS has now been used to explore the conditions for the ion beam extraction from a still nonexisting ion source, a so called ARC-ECRIS [P. Suominen and F. Wenander, Rev. Sci. Instrum. 79, 02A305 (2008)]. It has to be shown whether the plasma generator has similar properties like regular ECRIS. However, the emittance of the extracted beam seems to be much better compared to an ECRIS equipped with a hexapole.
Formulation of phase-field energies for microstructure in complex crystal structures
Authors: Yang Lun , Dayal Kaushik
Published: March 2010

The unusual properties of many multifunctional materials originate from a structural phase transformation and consequent martensitic microstructure. Phase-field models are typically used to predict the formation of microstructural patterns and subsequent evolution under applied loads. However, formulating a phase-field energy with the correct equilibrium crystal structures and that also respects the crystallographic symmetry is a formidable task in complex materials. This paper presents a simple method to construct such energy density functions for phase-field modeling. The method can handle complex equilibrium structures and crystallographic symmetry with ease. We demonstrate it on a shape memory alloy with 12 monoclinic variants.
Note: Toward multiple addressable optical trapping
Authors: Faustov Alexei R. , Webb Michael R. , Walt David R.
Published: March 2010

We describe a setup for addressable optical trapping in which a laser source is focused on a digital micromirror device and generates an optical trap in a microfluidic cell. In this paper, we report a proof-of-principle single beam/single micromirror/single three-dimensional trap arrangement that should serve as the basis for a multiple-trap instrument.
Physical mechanism of anisotropic sensitivity in pentaerythritol tetranitrate from compressive-shear reaction dynamics simulations
Authors: Zybin Sergey V. , Goddard William A. , Xu Peng , van Duin Adri C. T. , Thompson Aidan P.
Published: March 2010

We propose computational protocol (compressive shear reactive dynamics) utilizing the ReaxFF reactive force field to study chemical initiation under combined shear and compressive load. We apply it to predict the anisotropic initiation sensitivity observed experimentally for shocked pentaerythritol tetranitrate single crystals. For crystal directions known to be sensitive we find large stress overshoots and fast temperature increase that result in early bond-breaking processes whereas insensitive directions exhibit small stress overshoot, lower temperature increase, and little bond dissociation. These simulations confirm the model of steric hindrance to shear and capture the thermochemical processes dominating the phenomena of shear-induced chemical initiation.
Ramping up the Spallation Neutron Source beam power with the H− source using 0 mg Cs/day
Authors: Stockli M. P. , Han B. , Murray S. N. , Pennisi T. R. , Santana M. , Welton R. F.
Published: March 2010

This paper describes the ramp up of the beam power for the Spallation Neutron Source by ramping up the pulse length, the repetition rate, and the beam current emerging from the H− source. Starting out with low repetition rates (≤10 Hz) and short pulse lengths (≤0.2 ms), the H− source and low-energy beam transport delivered from Lawrence Berkeley National Laboratory exceeded the requirements with almost perfect availability. This paper discusses the modifications that were required to exceed 0.2 ms pulse length and 0.2% duty factor with acceptable availability and performance. Currently, the source is supporting neutron production at 1 MW with 38 mA linac beam current at 60 Hz and 0.9 ms pulse length. The pulse length will be increased to ∼1.1 ms to meet the requirements for neutron production with a power between 1 and 1.4 MW. A medium-energy beam transport (MEBT) beam current of 46 mA with a 5.4% duty factor has been demonstrated for 32 h. A 56 mA MEBT beam current with a 4.1% duty factor has been demonstrated for 20 min at the conclusion of a 12-day production run. This is close to the 59 mA needed for 3 MW neutron productions. Also notable is the Cs2CrO4 cesium system, which dispenses ∼10 mg of Cs during the startup of the ion source, sufficient for producing the required 38 mA for 4 weeks without significant degradation.
Multiple localized states in centrifugally stable rotating flow
Authors: Abshagen J. , Heise M. , Pfister G. , Mullin T.
Published: March 2010

We report experimental and numerical results from investigations into the onset of novel localized cellular states in the centrifugally stable regime of Taylor–Couette flow at sufficiently high rates of counter-rotation of the outer cylinder. Quantitative comparison is made between experimental results and those obtained from numerical bifurcation studies of the steady axisymmetric Navier–Stokes equations. The onset of the vortices is smooth but they appear over a narrow range of Reynolds number. This enables the use of a suitable measure to produce excellent quantitative agreement between calculation and experiment. The numerical methods are also used to uncover evidence for a homoclinic snake which indicates rich multiplicity in the steady solution set.
Coherent backscattering in optical microring resonators
Authors: Morichetti F. , Canciamilla A. , Martinelli M. , Samarelli A. , De La Rue R. M. , Sorel M. , Melloni A.
Published: March 2010

The effects of backscattering induced by waveguide sidewall roughness in integrated ring resonators (RRs) are experimentally observed. We demonstrate that coherent backscattering, originated by multiple round trips in the RR, increases with the square of the effective group index of the cavity and can dramatically affect the behavior of integrated RRs even at moderate quality factors of 104. From our results backscattering emerges as one of the most severe limiting factors on the performance of RRs fabricated with state-of-the-art silicon-on-insulator nanowaveguides.
Long-term impact of coordinated warren ripping programmes on rabbit populations
Authors: McPhee S. R. , Butler K. L.
Published: March 2010

Context. It is important to examine the long-term effectiveness of rabbit management programmes based on warren destruction using modern warren ripping machinery, at a time when the continuing impacts of both myxomatosis and rabbit haemorrhagic disease (RHD) may have reduced the capacity of rabbit populations to recover.
Aims. To determine the long-term effectiveness of coordinated warren ripping programmes in reducing rabbit densities and maintaining these low densities.
Methods. Commencing in 1998, 14 sites with coordinated warren ripping programmes and three sites without rabbit control were monitored within Victoria. Spotlight counts of rabbit numbers recorded before the spread of RHD and warren ripping were compared with numbers recorded from 2005 to 2008. The efficacy of coordinated warren ripping programmes was assessed in relation to the machinery used, the manner in which the warrens were ripped, the characteristics of the ripped areas and the impact of follow-up control.
Key results. Warren ripping programmes were very successful in reducing rabbit numbers for up to 10 years, whereas rabbit populations that were not managed returned to pre-RHD densities. The most effective warren ripping programmes, which reduced populations to 97% of the pre-RHD densities and maintained them at this level, used heavy, powerful ripping machinery to rip all warrens within 12 months. There was no evidence that the relationship between rabbit population decline and warren ripping was affected by the characteristics of the ripped areas or the follow-up control effort.
Conclusions. Following the spread of RHD in areas where warren ripping is practicable, well-managed ripping programmes provide an immediate solution for achieving and sustaining low rabbit populations.
Implications. The efficacy of RHD in regulating rabbit populations has diminished. The improvement of existing or the development of new biological control agents could take decades. In contrast, coordinated warren ripping programmes provide more predictable long-term reductions in rabbit populations.
Noncriterial Recollection Influences Metacognitive Monitoring and Control Processes
Authors: Brewer Gene A. , Marsh Richard L. , Clark-Foos Arlo , Meeks Joseph T.
Published: March 2010

When retrieving information from memory, temporarily irrelevant material may influence future retrieval endeavours. According to an accessibility account, the amount and intensity of this information can be used to predict the availability of related material. A dual-source paradigm was used to investigate whether information that was not relevant (i.e., noncriterial recollection) to the current memory search would influence metacognitive judgements about a relevant, criterial dimension. In two experiments, participants gave higher feelings-of-knowing judgements for a weakly encoded source dimension when they could subsequently recall the other source dimension later. Furthermore, the influence of the noncriterial information appeared to be driven more so by the subjective state of remembering rather than knowing. Thus, strong memorial information that is temporarily irrelevant influences behaviour.
Role of the Sinorhizobium meliloti Global Regulator Hfq in Gene Regulation and Symbiosis
Authors: Gao Mengsheng , Barnett Melanie J. , Long Sharon R. , Teplitski Max
Published: March 2010

The RNA-binding protein Hfq is a global regulator which controls diverse cellular processes in bacteria. To begin understanding the role of Hfq in the Sinorhizobium meliloti–Medicago truncatula nitrogen-fixing symbiosis, we defined free-living and symbiotic phenotypes of an hfq mutant. Over 500 transcripts were differentially accumulated in the hfq mutant of S. meliloti Rm1021 when grown in a shaking culture. Consistent with transcriptome-wide changes, the hfq mutant displayed dramatic alterations in metabolism of nitrogen-containing compounds, even though its carbon source utilization profiles were nearly identical to the wild type. The hfq mutant had reduced motility and was impaired for growth at alkaline pH. A deletion of hfq resulted in a reduced symbiotic efficiency, although the mutant was still able to initiate nodule development and differentiate into bacteroids.
Multiple Coat Protein Mutations Abolish Recognition of Pepino mosaic potexvirus (PepMV) by the Potato Rx Resistance Gene in Transgenic Tomatoes
Authors: Candresse Thierry , Marais Armelle , Faure Chantal , Dubrana Marie Pierre , Gombert Julie , Bendahmane Abdelhafid
Published: March 2010

Despite the fact that Pepino mosaic virus (PepMV) and Potato virus X (PVX) share less than 40% identity in their coat proteins (CP), the known PVX elicitor of Rx, transgenic tomato (cv. Microtom) plants expressing a functional potato Rx resistance gene showed resistance toward PepMV. However, in a low percentage of plants, PepMV accumulation was observed and back inoculation experiments demonstrated that these plants contained resistance-breaking PepMV variants. Sequencing of the CP gene of these variants showed the accumulation of mutations in the amino acid 41 to 125 region the CP, whereas no mutations were observed in the nonevolved isolates. Agroinfiltration-mediated transient expression of the mutant CP demonstrated that they had a greatly attenuated or abolished ability to induce a hypersensitive reaction in Rx-expressing Nicotiana benthamiana leaves. The transient expression of truncated forms of the PepMV CP allowed the identification of a minimal elicitor domain (amino acids 30 to 136). These results demonstrate that the Rx-based sensing system is able to recognize the PepMV CP but, contrary to the situation with PVX, for which only two closely spaced resistance-breaking mutations are known, many mutations over a significant stretch of the PepMV CP allow escape from recognition by Rx.
Complete Genome Sequence of the Fire Blight Pathogen Erwinia amylovora CFBP 1430 and Comparison to Other Erwinia spp.
Authors: Smits Theo H. M. , Rezzonico Fabio , Kamber Tim , Blom Jochen , Goesmann Alexander , Frey Jürg E. , Duffy Brion
Published: March 2010

Fire blight, caused by the enterobacterium Erwinia amylovora, is a devastating disease of rosaceous plants that has global economic importance for apple and pear production and trade. The complete genome of E. amylovora CFBP 1430 was sequenced, annotated, and compared with the genomes of other Erwinia spp. Several singleton and shared features of the E. amylovora CFBP 1430 genome were identified that offer a first view into evolutionary aspects within the genus Erwinia. Comparative genomics identified or clarified virulence and fitness determinants and secretion systems. Novel insights revealed in the genome of E. amylovora CFBP 1430 hold potential for exploitation to improve the design of more effective fire blight control strategies.
Different Domains of Phytophthora sojae Effector Avr4/6 Are Recognized by Soybean Resistance Genes Rps4 and Rps6
Authors: Dou Daolong , Kale Shiv D. , Liu Tingli , Tang Qinghua , Wang Xia , Arredondo Felipe D. , Basnayake Shiromi , Whisson Stephen , Drenth Andre , Maclean Don , Tyler Brett M.
Published: March 2010

At least 12 avirulence genes have been genetically identified and mapped in Phytophthora sojae, an oomycete pathogen causing root and stem rot of soybean. Previously, the Avr4 and Avr6 genes of P. sojae were genetically mapped within a 24 kb interval of the genome. Here, we identify Avr4 and Avr6 and show that they are actually a single gene, Avr4/6, located near the 24-kb region. Avr4/6 encodes a secreted protein of 123 amino acids with an RXLR-dEER protein translocation motif. Transient expression of Avr4/6 in soybean leaves revealed that its gene product could trigger a hypersensitive response (HR) in the presence of either Rps4 or Rps6. Silencing Avr4/6 in P. sojae stable transformants abolished the avirulence phenotype exhibited on both Rps4 and Rps6 soybean cultivars. The N terminus of Avr4/6, including the dEER motif, is sufficient to trigger Rps4-dependent HR while its C terminus is sufficient to trigger Rps6-mediated HR. Compared with alleles from avirulent races, alleles of Avr4/6 from virulent races possess nucleotide substitutions in the 5′ untranslated region of the gene but not in the protein-coding region.
Expression of BvGLP-1 Encoding a Germin-Like Protein from Sugar Beet in Arabidopsis thaliana Leads to Resistance Against Phytopathogenic Fungi
Authors: Knecht Katrin , Seyffarth Monique , Desel Christine , Thurau Tim , Sherameti Irena , Lou Binggan , Oelmüller Ralf , Cai Daguang
Published: March 2010

Nematode (Heterodera schachtii) resistance in sugar beet (Beta vulgaris) is controlled by a single dominant resistance gene, Hs1pro-1. BvGLP-1 was cloned from resistant sugar beet. The BvGLP-1 messenger (m)RNA is highly upregulated in the resistant plants after nematode infection, suggesting its role in the Hs1pro-1 mediated resistance. BvGLP-1 exhibits sequence homology to a set of plant germin-like proteins (GLP), from which several have proved to be functional in plant basal or defense resistance against fungal pathogens. To test whether BvGLP-1 is also involved in the plant–fungus interaction, we transferred BvGLP-1 into Arabidopsis and challenged the transgenic plants with the pathogenic fungi Verticillium longisporum and Rhizoctonia solani as well as with the beneficial endophytic fungus Piriformospora indica. The expression of BvGLP-1 in Arabidopsis elevated the H2O2 content and conferred significant resistance to V. longisporum and R. solani but did not affect the beneficial interaction with P. indica in seedlings. Microscopic observations revealed a dramatic reduction in the amount of hyphae of the pathogenic fungi on the root surface as well as of fungal mycelium developed inside the roots of transgenic Arabidopsis compared with wild-type plants. Molecular analysis demonstrated that the BvGLP-1 expression in Arabidopsis constitutively activates the expression of a subset of plant defense-related proteins such as PR-1 to PR-4 and PDF1.2 but not PDF2.1 and PDF2.3. In contrast, the PDF2.1 mRNA level was downregulated. These data suggest an important role of BvGLP-1 in establishment of plant defense responses, which follow specific signaling routes that diverge from those induced by the beneficial fungus.
Six New Genes Required for Production of T-Toxin, a Polyketide Determinant of High Virulence of Cochliobolus heterostrophus to Maize
Authors: Inderbitzin Patrik , Asvarak Thipa , Turgeon B. Gillian
Published: March 2010

Southern Corn Leaf Blight, one of the worst plant disease epidemics in modern history, was caused by Cochliobolus heterostrophus race T, which produces T-toxin, a determinant of high virulence to maize carrying Texas male sterile cytoplasm. The genetics of T-toxin production is complex and the evolutionary origin of associated genes is uncertain. It is known that ability to produce T-toxin requires three genes encoded at two unlinked loci, Tox1A and Tox1B, which map to the breakpoints of a reciprocal translocation. DNA associated with Tox1A and Tox1B sums to about 1.2 Mb of A+T rich, repeated DNA that is not found in less virulent race O or other Cochliobolus species. Here, we describe identification and targeted deletion of six additional genes, three mapping to Tox1A and three to Tox1B. Mutant screens indicate that all six genes are involved in T-toxin production and high virulence to maize. The nine known Tox1 genes encode two polyketide synthases (PKS), one decarboxylase, five dehydrogenases, and one unknown protein. Only two have a similar phylogenetic profile. To trace evolutionary history of one of the core PKS, DNA from more than 100 Dothideomycete species were screened for homologs. An ortholog (60% identity) was confirmed in Didymella zeae-maydis, which produces PM-toxin, a polyketide of similar structure and biological specificity as T-toxin. Only one additional Dothideomycete species, the dung ascomycete Delitschia winteri harbored a paralog. The unresolved evolutionary history and distinctive gene signature of the PKS (fast-evolving, discontinuous taxonomic distribution) leaves open the question of lateral or vertical transmission.
Evolution and Regulation of the Lotus japonicus LysM Receptor Gene Family
Authors: Lohmann Gitte Vestergaard , Shimoda Yoshikazu , Nielsen Mette Wibroe , Jørgensen Frank Grønlund , Grossmann Christina , Sandal Niels , Sørensen Kirsten , Thirup Søren , Madsen Lene Heegaard , Tabata Satoshi , Sato Shusei , Stougaard Jens , Radutoiu Simona
Published: March 2010

LysM receptor kinases were identified as receptors of acylated chitin (Nod factors) or chitin produced by plant-interacting microbes. Here, we present the identification and characterization of the LysM receptor kinase gene (Lys) family (17 members) in Lotus japonicus. Comprehensive phylogenetic analysis revealed a correlation between Lys gene structure and phylogeny. Further mapping coupled with sequence-based anchoring on the genome showed that the family has probably expanded by a combination of tandem and segmental duplication events. Using a sliding-window approach, we identified distinct regions in the LysM and kinase domains of recently diverged Lys genes where positive selection may have shaped ligand interaction. Interestingly, in the case of NFR5 and its closest paralog, LYS11, one of these regions coincides with the predicted Nod-factor binding groove and the suggested specificity determining area of the second LysM domain. One hypothesis for the evolutionary diversification of this receptor family in legumes is their unique capacity to decipher various structures of chitin-derived molecules produced by an extended spectrum of interacting organisms: symbiotic, associative, endophytic, and parasitic. In a detailed expression analysis, we found several Lotus Lys genes regulated not only during the symbiotic association with Mesorhizobium loti but also in response to chitin treatment.
Mechanical stress, fracture risk and beak evolution in Darwin's ground finches (
Geospiza
)
Authors: Soons Joris , Herrel Anthony , Genbrugge Annelies , Aerts Peter , Podos Jeffrey , Adriaens Dominique , de Witte Yoni , Jacobs Patric , Dirckx Joris
Published: March 2010

Darwin's finches have radiated from a common ancestor into 14 descendent species, each specializing on distinct food resources and evolving divergent beak forms. Beak morphology in the ground finches (
Geospiza
) has been shown to evolve via natural selection in response to variation in food type, food availability and interspecific competition for food. From a mechanical perspective, however, beak size and shape are only indirectly related to birds' abilities to crack seeds, and beak form is hypothesized to evolve mainly under selection for fracture avoidance. Here, we test the fracture-avoidance hypothesis using finite-element modelling. We find that across species, mechanical loading is similar and approaches reported values of bone strength, thus suggesting pervasive selection on fracture avoidance. Additionally, deep and wide beaks are better suited for dissipating stress than are more elongate beaks when scaled to common sizes and loadings. Our results illustrate that deep and wide beaks in ground finches enable reduction of areas with high stress and peak stress magnitudes, allowing birds to crack hard seeds while limiting the risk of beak failure. These results may explain strong selection on beak depth and width in natural populations of Darwin's finches.
Acoustic discrimination of sympatric morphs in Darwin's finches: a behavioural mechanism for assortative mating?
Authors: Podos Jeffrey
Published: March 2010

Populations with multiple morphological or behavioural types provide unique opportunities for studying the causes and consequences of evolutionary diversification. A population of the medium ground finch (Geospiza fortis) at El Garrapatero on Santa Cruz Island, Galápagos, features two beak size morphs. These morphs produce acoustically distinctive songs, are subject to disruptive selection and mate assortatively by morph. The main goal of the present study was to assess whether finches from this population are able to use song as a cue for morph discrimination. A secondary goal of this study was to evaluate whether birds from this population discriminate songs of their own locality versus another St Cruz locality, Borrero Bay, approximately 24 km to the NW. I presented territorial males with playback of songs of their own morph, of the other morph, and of males from Borrero Bay. Males responded more strongly to same-morph than to other-morph playbacks, showing significantly shorter latencies to flight, higher flight rates and closer approaches to the playback speaker. By contrast, I found only minor effects of locality on responsiveness. Evidence for morph discrimination via acoustic cues supports the hypothesis that song can serve as a behavioural mechanism for assortative mating and sympatric evolutionary divergence.
Divergence with gene flow as facilitated by ecological differences: within-island variation in Darwin's finches
Authors: de León Luis Fernando , Bermingham Eldredge , Podos Jeffrey , Hendry Andrew P.
Published: March 2010

Divergence and speciation can sometimes proceed in the face of, and even be enhanced by, ongoing gene flow. We here study divergence with gene flow in Darwin's finches, focusing on the role of ecological/adaptive differences in maintaining/promoting divergence and reproductive isolation. To this end, we survey allelic variation at 10 microsatellite loci for 989 medium ground finches (Geospiza fortis) on Santa Cruz Island, Galápagos. We find only small genetic differences amongG. fortisfrom different sites. We instead find noteworthy genetic differences associated with beak. Moreover,G. fortisat the site with the greatest divergence in beak size also showed the greatest divergence at neutral markers; i.e. the lowest gene flow. Finally, morphological and genetic differentiation between theG. fortisbeak-size morphs was intermediate to that betweenG. fortisand its smaller (Geospiza fuliginosa) and larger (Geospiza magnirostris) congeners. We conclude that ecological differences associated with beak size (i.e. foraging) influence patterns of gene flow withinG. fortison a single island, providing additional support for ecological speciation in the face of gene flow. Patterns of genetic similarity within and between species also suggest that interspecific hybridization might contribute to the formation of beak-size morphs withinG. fortis.
A degron created by SMN2 exon 7 skipping is a principal contributor to spinal muscular atrophy severity
Authors: Cho Sungchan , Dreyfuss Gideon
Published: March 2010

Spinal muscular atrophy (SMA) is caused by homozygous survival of motor neurons 1 (SMN1) gene deletions, leaving a duplicate gene, SMN2, as the sole source of SMN protein. However, most of the mRNA produced from SMN2 pre-mRNA is exon 7-skipped (∼80%), resulting in a highly unstable and almost undetectable protein (SMNΔ7). We show that this splicing defect creates a potent degradation signal (degron; SMNΔ7-DEG) at SMNΔ7's C-terminal 15 amino acids. The S270A mutation inactivates SMNΔ7-DEG, generating a stable SMNΔ7 that rescues viability of SMN-deleted cells. These findings explain a key aspect of the SMA disease mechanism, and suggest new treatment approaches based on interference with SMNΔ7-DEG activity.
G-less Cassette In Vitro Transcription Using HeLa Cell Nuclear Extracts
Authors: Carey Michael F. , Peterson Craig L. , Smale Stephen T.
Published: March 2010

INTRODUCTION

The G-less cassette is a 365-nucleotide (nt) segment of DNA lacking guanine (G) residues on the nontemplate strand. In principle, a full-length transcript can be generated in an in vitro reaction lacking GTP, an omission that leads to suppression of most random, nonspecific transcription throughout the plasmid. This method, like runoff transcription, generates radiolabeled RNA products, directly bypassing the necessity and extra time required to perform primer extension or other indirect mRNA product measurements. Unlike runoff transcription, which requires a cleaved end, the G-less assay can be performed on a circular, supercoiled plasmid, which in many systems is a more efficient template. In practice, most crude systems, such as HeLa nuclear extracts, contain low amounts of contaminating GTP that lead to small amounts of background transcription and occasionally can cause random upstream transcription to read through the G-less cassette. To minimize these artifacts, the reaction generally contains 3′-O-Me-GTP, a chain-terminating analog of GTP that causes transcription to cease when it is incorporated into a growing transcript, much like the dideoxy analogs used in DNA sequencing. The reaction products are cleaved with T1 RNase, which cleaves RNAs at G residues, further reducing background transcription; the G-less mRNA remains intact, whereas small random RNAs are digested.
Suspended Embryo Mount for Imaging Caenorhabditis elegans
Authors: Mohler William A. , Isaacson Ariel B.
Published: March 2010

INTRODUCTION

This protocol describes the preparation of Caenorhabditis elegans embryos for four-dimensional (4D) imaging. Embryos are excised from gravid hermaphrodites and allowed to adhere directly to a poly-L-lysine-coated coverslip. The coverslip is then used to create a slide chamber in which the embryos are suspended in buffer. These suspended mounts are better for 4D recordings than agar mounts because, although agar mounts produce more uniformly oriented embryos, evaporation from the agar pads tends to shift the embryos gradually over time. 4D spatial registration with suspended mounts is quite stable, and it is possible to digitally reorient embryos within the recorded volume of the three-dimensional (3D) stack during post-processing of the data.
Preparation and Orcein Staining of Mitotic Chromosomes from Drosophila Larval Brain
Authors: Pimpinelli Sergio , Bonaccorsi Silvia , Fanti Laura , Gatti Maurizio
Published: March 2010

INTRODUCTION

In this protocol, larval brains from Drosophila are incubated in vitro with colchicine, treated with hypotonic solution, fixed, and squashed in aceto-orcein. This procedure provides a large number of well-spread metaphase figures (200-400 per brain) that can be analyzed for chromosome morphology, the presence of chromosome aberrations, and the degree of ploidy.
Chromosome Banding of Mitotic Chromosomes from Drosophila Larval Brain: Figure 1.
Authors: Pimpinelli Sergio , Bonaccorsi Silvia , Fanti Laura , Gatti Maurizio
Published: March 2010

INTRODUCTION

The classical chromosome-banding techniques developed for mammalian chromosomes do not differentiate the euchromatic arms of Drosophila mitotic chromosomes. However, some of these techniques produce a sharp and highly reproducible banding of Drosophila heterochromatin. For example, the use of quinacrine-, Hoechst-, and N-banding differentiates Drosophila heterochromatin into 61 cytological entities, allowing precise localization of heterochromatic breakpoints. These banding techniques can also be successfully used to differentiate mitotic heterochromatin of various Drosophila and mosquito species. Here we present protocols routinely used in our laboratories for chromosome banding, including the use of Hoechst, 4′,6-diamidino-2-phenylindole (DAPI), quinacrine, and Giemsa stains.
Immunoelectron Microscopy Analysis of Recombinant Baculovirus Display Viruses
Authors: Mäkelä Anna R. , Ernst Wolfgang , Grabherr Reingard , Oker-Blom Christian
Published: March 2010

INTRODUCTION

The baculovirus expression vector system has been used extensively to produce numerous proteins originating from both prokaryotic and eukaryotic sources. In addition to easy cloning techniques and abundant viral propagation, the system’s insect cell environment provides eukaryotic post-translational modification machinery. The baculovirus display vector system provides a number of advantages over prokaryotic systems, allowing the combination of genotype with phenotype, enabling presentation of foreign peptides or even complex proteins on the baculoviral envelope or capsid. Baculoviruses permit larger gene insertions, are easily propagated, and can be grown to high titers. Furthermore, surface modifications of the viral capsid enable specific targeting. This strategy can be used to enhance viral binding and entry to a wide variety of both dividing and nondividing mammalian cells, as well as to produce antibodies against the displayed antigen. In addition, the technology should enable modifications of intracellular behavior, i.e., trafficking of recombinant “nanoparticles,” a highly relevant feature for studies of targeted gene or protein delivery. After generating the display viral stock, it is important to confirm the presence and functionality of the displayed peptides or proteins on the viral particles before proceeding to further experiments. Accordingly, infected insect cells and budded virions can be analyzed by a variety of methods using appropriate antibodies. This protocol describes a standard immunoelectron microscopy technique in detail.
Monitoring Baculovirus-Mediated Efficiency of Gene Delivery
Authors: Mäkelä Anna R. , Ernst Wolfgang , Grabherr Reingard , Oker-Blom Christian
Published: March 2010

INTRODUCTION

The baculovirus expression vector system has been used extensively to produce numerous proteins originating from both prokaryotic and eukaryotic sources. In addition to easy cloning techniques and abundant viral propagation, the system’s insect cell environment provides eukaryotic post-translational modification machinery. The baculovirus display vector system provides a number of advantages over prokaryotic systems, allowing the combination of genotype with phenotype, enabling presentation of foreign peptides or even complex proteins on the baculoviral envelope or capsid. Baculoviruses permit larger gene insertions, are easily propagated, and can be grown to high titers. Furthermore, surface modifications of the viral capsid enable specific targeting. This strategy can be used to enhance viral binding and entry to a wide variety of both dividing and nondividing mammalian cells, as well as to produce antibodies against the displayed antigen. In addition, the technology should enable modifications of intracellular behavior, that is, trafficking of recombinant “nanoparticles,” a highly relevant feature for studies of targeted gene or protein delivery. Also, the ability to incorporate reporter genes under transcriptional regulation of mammalian promoters enables transduction efficiency to be monitored in mammalian cells in vitro and in tissues in vivo. Luciferase molecules in particular are nontoxic and emit light in direct proportion to their number in mammalian cells. This provides a sensitive and rapid assay for quantification of transgene expression without the need for illumination with an external excitation source.