Sequencing the potato genome: outline and first results to come from the elucidation of the sequence of the world's third most important food crop

Potato is a member of the Solanaceae, a plant family that includes several other economically important species, such as tomato, eggplant, petunia, tobacco and pepper. The Potato Genome Sequencing Consortium (PGSC) aims to elucidate the complete genome sequence of potato, the third most important food crop in the world. The PGSC is a collaboration between 13 research groups from China, India, Poland, Russia, the Netherlands, Ireland, Argentina, Brazil, Chile, Peru, USA, New Zealand and the UK. The potato genome consists of 12 chromosomes and has a (haploid) length of approximately 840 million base pairs, making it a medium-sized plant genome. The sequencing project builds on a diploid potato genomic bacterial artificial chromosome (BAC) clone library of 78000 clones, which has been fingerprinted and aligned into ~7000 physical map contigs. In addition, the BAC-ends have been sequenced and are publicly available. Approximately 30000 BACs are anchored to the Ultra High Density genetic map of potato, composed of 10000 unique AFLPTM markers. From this integrated genetic-physical map, between 50 to 150 seed BACs have currently been identified for every chromosome. Fluorescent in situ hybridization experiments on selected BAC clones confirm these anchor points. The seed clones provide the starting point for a BAC-by-BAC sequencing strategy. This strategy is being complemented by whole genome shotgun sequencing approaches using both 454 GS FLX and Illumina GA2 instruments. Assembly and annotation of the sequence data will be performed using publicly available and tailor-made tools. The availability of the annotated data will help to characterize germplasm collections based on allelic variance and to assist potato breeders to more fully exploit the genetic potential of potat

Overestimated biomass carbon pools of the northern mid- and high latitude forests

The biomass carbon (C) stock of forests is one of key parameters for the study of regional and global carbon cycles. Literature reviews shows that inventory-based forest C stocks documented for major countries in the middle and high northern latitudes fall within a narrow range of 36-56 Mg C ha(-1) with an overall area-weighted mean of 43.6 Mg C ha(-1). These estimates are 0.40 to 0.71 times smaller than those (61-108 Mg C ha(-1)) used in previous analysis of balancing the global carbon budget. A statistical analysis, using the global forest biomass database, implies that aboveground biomass per hectare is proportional to forest mean height [biomass in Mg/ha = 10.63 (height in m)] in closed-canopy forests in the study regions, indicating that forest height can be a proxy of regional biomass C stocks. The narrow range of C stocks is likely a result of similar forest height across the northern regions. The lower biomass C stock obtained in this study strongly suggests that the role of the northern forests in the global carbon cycle needs to be re-evaluated. Our findings also suggest that regional estimates of biomass could be readily made from the use of satellite methods such as lidar that can measure forest canopy height over large regions

Physiological genetics of aluminum tolerance in the wheat cultivar Atlas 66

Aluminum toxicity limits wheat (Triticum aestivum L.) production on acidic soils. The wheat cultivar Atlas 66 reportedly may have both more than one Al tolerance gene and more than one Al tolerance mechanism. The purpose of this study was to identify the Al tolerance mechanisms conferred by the individual Atlas 66 Al tolerance genes present in near-isogenic lines (NILs) of the cv. Century and Chisholm ('Century-T' and 'Chisholm-T'). Seedling hydroponic culture analysis revealed that the NILs were not as Al tolerant, nor were they able to exclude Al from root apices as effectively as Atlas 66. Al-inducible malate release from root apices was significantly higher in the NILs compared with the recurrent parents, but less than that observed in Atlas 66. In contrast, root phosphate release was significantly lower than previously reported in Atlas 66, with no major differences observed among lines. These results indicate that the Atlas 66 Al tolerance gene present in each NIL acts by increasing Al-inducible malate release from root tips, but confers only a portion of the Al tolerance of Atlas 66 in both instances. Thus, differences in Al tolerance between the NILs and Atlas 66 can be attributed to malate release differences, and not differential phosphate release. Further, these results indicate that genetic variation at more than one locus underlies the malate- mediated Al tolerance differences in Atlas 66, when compared with Century and Chisholm. The Atlas 66 alleles for these loci have not been introgressed into the NILs.Peer reviewedPlant and Soil Science

Ab initio and finite-temperature molecular dynamics studies of lattice resistance in tantalum

This manuscript explores the apparent discrepancy between experimental data and theoretical calculations of the lattice resistance of bcc tantalum. We present the first results for the temperature dependence of the Peierls stress in this system and the first ab initio calculation of the zero-temperature Peierls stress to employ periodic boundary conditions, which are those best suited to the study of metallic systems at the electron-structure level. Our ab initio value for the Peierls stress is over five times larger than current extrapolations of experimental lattice resistance to zero-temperature. Although we do find that the common techniques for such extrapolation indeed tend to underestimate the zero-temperature limit, the amount of the underestimation which we observe is only 10-20%, leaving open the possibility that mechanisms other than the simple Peierls stress are important in controlling the process of low temperature slip.Comment: 12 pages and 9 figure

Discrete cilia modelling with singularity distributions

We discuss in detail techniques for modelling flows due to finite and infinite arrays of beating cilia. An efficient technique, based on concepts from previous ‘singularity models’ is described, that is accurate in both near and far-fields. Cilia are modelled as curved slender ellipsoidal bodies by distributing Stokeslet and potential source dipole singularities along their centrelines, leading to an integral equation that can be solved using a simple and efficient discretisation. The computed velocity on the cilium surface is found to compare favourably with the boundary condition. We then present results for two topics of current interest in biology. 1) We present the first theoretical results showing the mechanism by which rotating embryonic nodal cilia produce a leftward flow by a ‘posterior tilt,’ and track particle motion in an array of three simulated nodal cilia. We find that, contrary to recent suggestions, there is no continuous layer of negative fluid transport close to the ciliated boundary. The mean leftward particle transport is found to be just over 1 μm/s, within experimentally measured ranges. We also discuss the accuracy of models that represent the action of cilia by steady rotlet arrays, in particular, confirming the importance of image systems in the boundary in establishing the far-field fluid transport. Future modelling may lead to understanding of the mechanisms by which morphogen gradients or mechanosensing cilia convert a directional flow to asymmetric gene expression. 2) We develop a more complex and detailed model of flow patterns in the periciliary layer of the airway surface liquid. Our results confirm that shear flow of the mucous layer drives a significant volume of periciliary liquid in the direction of mucus transport even during the recovery stroke of the cilia. Finally, we discuss the advantages and disadvantages of the singularity technique and outline future theoretical and experimental developments required to apply this technique to various other biological problems, particularly in the reproductive system

Identified particles in Au+Au collisions at sqrt{s_NN} = 200 GeV

The yields of identified particles have been measured at RHIC for Au+Au collisions at sqrt{s_NN} = 200 GeV using the PHOBOS spectrometer. The ratios of antiparticle to particle yields near mid-rapidity are presented. The first measurements of the invariant yields of charged pions, kaons and protons at very low transverse momenta are also shown.Comment: 4 pages, 4 figures, Contribution to Quark Matter 2002, Nantes, France, July 200

Universal Behavior of Charged Particle Production in Heavy Ion Collisions

The PHOBOS experiment at RHIC has measured the multiplicity of primary charged particles as a function of centrality and pseudorapidity in Au+Au collisions at sqrt(s_NN) = 19.6, 130 and 200 GeV. Two kinds of universal behavior are observed in charged particle production in heavy ion collisions. The first is that forward particle production, over a range of energies, follows a universal limiting curve with a non-trivial centrality dependence. The second arises from comparisons with pp/pbar-p and e+e- data. N_tot/(N_part/2) in nuclear collisions at high energy scales with sqrt(s) in a similar way as N_tot in e+e- collisions and has a very weak centrality dependence. This feature may be related to a reduction in the leading particle effect due to the multiple collisions suffered per participant in heavy ion collisions.Comment: 4 Pages, 5 Figures, contributed to the Proceedings of Quark Matter 2002, Nantes, France, 18-24 July 200

Numerical study of the thermoelectric power factor in ultra-thin Si nanowires

Low dimensional structures have demonstrated improved thermoelectric (TE) performance because of a drastic reduction in their thermal conductivity, {\kappa}l. This has been observed for a variety of materials, even for traditionally poor thermoelectrics such as silicon. Other than the reduction in {\kappa}l, further improvements in the TE figure of merit ZT could potentially originate from the thermoelectric power factor. In this work, we couple the ballistic (Landauer) and diffusive linearized Boltzmann electron transport theory to the atomistic sp3d5s*-spin-orbit-coupled tight-binding (TB) electronic structure model. We calculate the room temperature electrical conductivity, Seebeck coefficient, and power factor of narrow 1D Si nanowires (NWs). We describe the numerical formulation of coupling TB to those transport formalisms, the approximations involved, and explain the differences in the conclusions obtained from each model. We investigate the effects of cross section size, transport orientation and confinement orientation, and the influence of the different scattering mechanisms. We show that such methodology can provide robust results for structures including thousands of atoms in the simulation domain and extending to length scales beyond 10nm, and point towards insightful design directions using the length scale and geometry as a design degree of freedom. We find that the effect of low dimensionality on the thermoelectric power factor of Si NWs can be observed at diameters below ~7nm, and that quantum confinement and different transport orientations offer the possibility for power factor optimization.Comment: 42 pages, 14 figures; Journal of Computational Electronics, 201