Chromosome-scale reference genome assembly of a diploid potato clone derived from an elite variety.

Potato (Solanum tuberosum L.) is one of the most important crops with a worldwide production of 370 million metric tons. The objectives of this study were (1) to create a high-quality consensus sequence across the two haplotypes of a diploid clone derived from a tetraploid elite variety and assess the sequence divergence from the available potato genome assemblies, as well as among the two haplotypes; (2) to evaluate the new assembly's usefulness for various genomic methods; and (3) to assess the performance of phasing in diploid and tetraploid clones, using linked-read sequencing technology. We used PacBio long reads coupled with 10x Genomics reads and proximity ligation scaffolding to create the dAg1_v1.0 reference genome sequence. With a final assembly size of 812 Mb, where 750 Mb are anchored to 12 chromosomes, our assembly is larger than other available potato reference sequences and high proportions of properly paired reads were observed for clones unrelated by pedigree to dAg1. Comparisons of the new dAg1_v1.0 sequence to other potato genome sequences point out the high divergence between the different potato varieties and illustrate the potential of using dAg1_v1.0 sequence in breeding applications.

Genome-Based Prediction of Time to Curd Induction in Cauliflower.

The development of cauliflower (Brassica oleracea var. botrytis) is highly dependent on temperature due to vernalization requirements, which often causes delay and unevenness in maturity during months with warm temperatures. Integrating quantitative genetic analyses with phenology modeling was suggested to accelerate breeding strategies toward wide-adaptation cauliflower. The present study aims at establishing a genome-based model simulating the development of doubled haploid (DH) cauliflower lines to predict time to curd induction of DH lines not used for model parameterization and test hybrids derived from the bi-parental cross. Leaf appearance rate and the relation between temperature and thermal time to curd induction were examined in greenhouse trials on 180 DH lines at seven temperatures. Quantitative trait loci (QTL) analyses carried out on model parameters revealed ten QTL for leaf appearance rate (LAR), five for the slope and two for the intercept of linear temperature-response functions. Results of the QTL-based phenology model were compared to a genomic selection (GS) model. Model validation was carried out on data comprising four field trials with 72 independent DH lines, 160 hybrids derived from the parameterization set, and 34 hybrids derived from independent lines of the population. The QTL model resulted in a moderately accurate prediction of time to curd induction (R2 = 0.42-0.51) while the GS model generated slightly better results (R2 = 0.52-0.61). Predictions of time to curd induction of test hybrids from independent DH lines were less precise with R2 = 0.40 for the QTL and R2 = 0.48 for the GS model. Implementation of juvenile-to-adult phase transition is proposed for model improvement.

On the Stability and Abundance of Single Walled Carbon Nanotubes.

Many nanotechnological applications, using single-walled carbon nanotubes (SWNTs), are only possible with a uniform product. Thus, direct control over the product during chemical vapor deposition (CVD) growth of SWNT is desirable, and much effort has been made towards the ultimate goal of chirality-controlled growth of SWNTs. We have used density functional theory (DFT) to compute the stability of SWNT fragments of all chiralities in the series representing the targeted products for such applications, which we compare to the chiralities of the actual CVD products from all properly analyzed experiments. From this comparison we find that in 84% of the cases the experimental product represents chiralities among the most stable SWNT fragments (within 0.2 eV) from the computations. Our analysis shows that the diameter of the SWNT product is governed by the well-known relation to size of the catalytic nanoparticles, and the specific chirality is normally determined by the product's relative stability, suggesting thermodynamic control at the early stage of product formation. Based on our findings, we discuss the effect of other experimental parameters on the chirality of the product. Furthermore, we highlight the possibility to produce any tube chirality in the context of recent published work on seeded-controlled growth.

Adsorption and reactions of O2 and D2 on small free palladium clusters in a cluster-molecule scattering experiment.

The adsorption of oxygen and hydrogen (deuterium) on small neutral palladium clusters was investigated in a cluster beam experiment. The beam passes through two low-pressure reaction cells, and the clusters, with and without adsorbed molecules, are detected using laser ionization and mass spectrometry. Both H(2) and O(2) adsorb efficiently on the palladium clusters with only moderate variations with cluster size in the investigated range, i.e. between 8 and 28 atoms. The co-adsorption of H(2) and O(2) results in the formation of H(2)O, detected as a decrease in the number of adsorbed oxygen atoms with an increasing number of collisions with H(2) molecules. A comparison is done with an earlier similar study of clusters of Pt. Furthermore a comparison is done with what is known for sticking and reactivity of surfaces.

Changes in single-walled carbon nanotube chirality during growth and regrowth.

A simple model for joining two single-walled carbon nanotubes (SWNTs) with different, arbitrary chiralities is used to systematically label junction structures which contain pentagon-heptagon pairs. The model is also used, together with density functional theory, to study the energetics of diameter and chirality changes of thin SWNTs during catalyzed growth or regrowth. We choose zigzag and armchair SWNTs attached to a Ni(55) cluster for our case studies.

The importance of strong carbon-metal adhesion for catalytic nucleation of single-walled carbon nanotubes.

Density functional theory is used to show that the adhesion between single-walled carbon nanotubes (SWNTs) and the catalyst particles from which they grow needs to be strong to support nanotube growth. It is found that Fe, Co, and Ni, commonly used to catalyze SWNT growth, have larger adhesion strengths to SWNTs than Cu, Pd, and Au and are therefore likely to be more efficient for supporting growth. The calculations also show that to maintain an open end of the SWNT it is necessary that the SWNT adhesion strength to the metal particle is comparable to the cap formation energy of the SWNT end. This implies that the difference between continued and discontinued SWNT growth to a large extent depends on the carbon-metal binding strength, which we demonstrate by molecular dynamics (MD) simulations. The results highlight that first principles computations are vital for the understanding of the binding strength's role in the SWNT growth mechanism and are needed to get accurate force field parameters for MD.

Computational studies of small carbon and iron-carbon systems relevant to carbon nanotube growth.

Density functional theory (DFT) calculations show that dimers and longer carbon strings are more stable than individual atoms on Fe(111) surfaces. It is therefore necessary to consider the formation of these species on the metal surfaces and their effect on the mechanism of single-walled nanotube (SWNT) growth. The good agreement between the trends (energies and structures) obtained using DFT and those based on the Brenner and AIREBO models indicate that these analytic models provide adequate descriptions of the supported carbon systems needed for valid molecular dynamics simulations of SWNT growth. In contrast, the AIREBO model provides a better description of the relative energies for isolated carbon species, and this model is preferred over the Brenner potential when simulating SWNT growth in the absence of metal particles. However, the PM3 semiempirical model appears to provide an even better description for these systems and, given sufficient computer resources, direct dynamics methods based on this model may be preferred.

Determination of OH number densities outside of a platinum catalyst using cavity ringdown spectroscopy.

It is demonstrated that cavity ringdown spectroscopy (CRDS) can be used to probe reaction intermediates desorbing from the surface during a heterogeneous catalytic reaction and provide information valuable in understanding the reaction kinetics. During water formation from H2 and O2, desorbed OH molecules outside of a polycrystalline platinum catalyst were quantified as a function of the relative hydrogen concentration, alphaH2 using CRDS. The temperature of the catalyst was 1500 K, the total pressure was 26 Pa, and the flow was set to 100 sccm. At a distance of 6.5 mm from the Pt catalyst, the maximum OH concentration was found to be 1.5+/-0.2x10(12) cm(-3) at an alphaH2 value of 10%, and the rotational temperature was determined to be 775+/-24 K. The desorbed OH molecules were also probed using laser-induced fluorescence (LIF), and the alphaH2-dependent OH abundance was compared with the CRDS results. The relative concentration of OH probed with LIF appeared to be lower at alphaH2=30-50% compared to what was determined by CRDS. The observed discrepancy is suggested to be due to electronic quenching, as was indicated by a shorter fluorescence lifetime at alphaH2=30% compared to at alphaH2=10%.

Photostability of commercial sunscreens upon sun exposure and irradiation by ultraviolet lamps.

BACKGROUND: Sunscreens are being widely used to reduce exposure to harmful ultraviolet (UV) radiation. The fact that some sunscreens are photounstable has been known for many years. Since the UV-absorbing ingredients of sunscreens may be photounstable, especially in the long wavelength region, it is of great interest to determine their degradation during exposure to UV radiation. Our aim was to investigate the photostability of seven commercial sunscreen products after natural UV exposure (UVnat) and artificial UV exposure (UVart). METHODS: Seven commercial sunscreens were studied with absorption spectroscopy. Sunscreen product, 0.5 mg/cm2, was placed between plates of silica. The area under the curve (AUC) in the spectrum was calculated for UVA (320-400 nm), UVA1 (340-400 nm), UVA2 (320-340 nm) and UVB (290-320 nm) before (AUCbefore) and after (AUCafter) UVart (980 kJ/m2 UVA and 12 kJ/m2 of UVB) and before and after UVnat. If theAUC Index (AUCI), defined as AUCI = AUCafter/AUCbefore, was > 0.80, the sunscreen was considered photostable. RESULTS: Three sunscreens were unstable after 90 min of UVnat; in the UVA range the AUCI was between 0.41 and 0.76. In the UVB range one of these sunscreens was unstable with an AUCI of 0.75 after 90 min. Three sunscreens were photostable after 120 min of UVnat; in the UVA range the AUCI was between 0.85 and 0.99 and in the UVB range between 0.92 and 1.0. One sunscreen showed in the UVA range an AUCI of 0.87 after UVnat but an AUCI of 0.72 after UVart. Five of the sunscreens were stable in the UVB region. CONCLUSION: The present study shows that several sunscreens are photounstable in the UVA range after UVnat and UVart. There is a need for a standardized method to measure photostability, and the photostability should be marked on the sunscreen product.

Atomistic simulations of catalyzed carbon nanotube growth.

We review the advances made in understanding the mechanism of catalyzed carbon nanotube growth, with the main focus on direct dynamics and molecular dynamics studies of single-walled carbon nanotube (SWNT) growth. These studies have deepened our understanding of the catalytic SWNT nucleation and growth mechanisms, but more accurate and efficient methods are required for a complete investigation at experimental growth conditions.

Graphitic encapsulation of catalyst particles in carbon nanotube production.

A new model is proposed for the encapsulation of catalyst metal particles by graphite layers that are obtained, for example, in low-temperature chemical vapor deposition production of carbon nanotubes (CNTs). In this model graphite layers are primarily formed from the dissolved carbon atoms in the metal-carbide particle when the particle cools. This mechanism is in good agreement with molecular dynamics simulations (which show that precipitated carbon atoms preferentially form graphite sheets instead of CNTs at low temperatures) and experimental results (e.g., encapsulated metal particles are found in low-temperature zones and CNTs in high-temperature regions of production apparatus, very small catalyst particles are generally not encapsulated, and the ratio of the number of graphitic layers to the diameter of the catalyst particle is typically 0.25 nm(-1)).

Bispectral fluorescence imaging combined with texture analysis and linear discrimination for correlation with histopathologic extent of basal cell carcinoma.

Fluorescence imaging has been shown to be a potential complement to visual inspection for demarcation of basal cell carcinoma (BCC), which is the most common type of skin cancer. Earlier studies have shown promising results when combining autofluorescence with protoporphyrin IX (Pp IX) fluorescence, induced by application of delta-5-aminolaevulinic acid (ALA). In this work, we have tried to further improve the ability of this technique to discriminate between areas of tumor and normal skin by implementing texture analysis and Fisher linear discrimination (FLD) on bispectral fluorescence data of BCCs located on the face. Classification maps of the lesions have been obtained from histopathologic mapping of the excised tumors. The contrast feature obtained from co-occurrence matrices was found to provide useful information, particularly for the ALA-induced Pp IX fluorescence data. Moreover, the neighborhood average features of both autofluorescence and Pp IX fluorescence were preferentially included in the analysis. The algorithm was trained by using a training set of images with good agreement with histopathology, which improved the discriminability of the validation set. In addition, cross validation of the training set showed good discriminability. Our results imply that FLD and texture analysis are preferential for correlation between bispectral fluorescence images and the histopathologic extension of the tumors.

Lipid cubic phases for improved topical drug delivery in photodynamic therapy.

We have evaluated the efficacy of lipid cubic phases, highly ordered self-assembly systems on the nanometer level, as drug delivery vehicles for in vivo topical administration of delta-aminolevulinic acid (ALA) and its methyl ester (m-ALA) on nude mice skin. ALA, a precursor of heme, induces the production of the photosensitizer protoporphyrin IX (PpIX) in living tissue. Measuring the PpIX fluorescence at the skin surface, after topical administration, makes indirect quantification of the penetration of ALA into the tissue possible. Cubic phases were formed of lipid (monoolein or phytantriol), water and drug. In some cases, propylene glycol was included in the cubic phase as well. The drug concentration was 3% (w/w, based on the total sample weight) in all investigated vehicles. When the formulations were applied for 1 h, the monoolein cubic systems and the three-component phytantriol sample showed higher fluorescence compared to the standard ointment during the 10 h of measurement. Both ALA and m-ALA yielded similar results, although the differences between the investigated vehicles were more pronounced when using m-ALA. For the 24-h applications, the monoolein cubic systems with m-ALA showed faster PpIX formation than the standard ointment, implying higher PpIX levels at short application times (less than 4 h). The systemic PpIX fluorescence of ALA was elevated by using the lipid cubic formulations. Notably, a small systemic effect was also observed for the monoolein cubic sample with m-ALA. These results imply improved PpIX formation when using the lipid cubic systems, most probably due to enhanced drug penetration.

Atom collision-induced resistivity of carbon nanotubes.

We report the observation of unusually strong and systematic changes in the electron transport in metallic single-walled carbon nanotubes that are undergoing collisions with inert gas atoms or small molecules. At fixed gas temperature and pressure, changes in the resistance and thermopower of thin films are observed that scale as roughly M(1/3), where M is the mass of the colliding gas species (He, Ar, Ne, Kr, Xe, CH4, and N2). Results of molecular dynamics simulations are also presented that show that the maximum deformation of the tube wall upon collision and the total energy transfer between the colliding atom and the nanotube also exhibit a roughly M(1/3) dependence. It appears that the transient deformation (or dent) in the tube wall may provide a previously unknown scattering mechanism needed to explain the atom collision-induced changes in the electrical transport.

Molecular dynamics study of the catalyst particle size dependence on carbon nanotube growth.

The molecular dynamics method, based on an empirical potential energy surface, was used to study the effect of catalyst particle size on the growth mechanism and structure of single-walled carbon nanotubes (SWNTs). The temperature for nanotube nucleation (800-1100 K), which occurs on the surface of the cluster, is similar to that used in catalyst chemical vapor deposition experiments, and the growth mechanism, which is described within the vapor-liquid-solid model, is the same for all cluster sizes studied here (iron clusters containing between 10 and 200 atoms were simulated). Large catalyst particles, which contain at least 20 iron atoms, nucleate SWNTs that have a far better tubular structure than SWNTs nucleated from smaller clusters. In addition, the SWNTs that grow from the larger clusters have diameters that are similar to the cluster diameter, whereas the smaller clusters, which have diameters less than 0.5 nm, nucleate nanotubes that are approximately 0.6-0.7 nm in diameter. This is in agreement with the experimental observations that SWNT diameters are similar to the catalyst particle diameter, and that the narrowest free-standing SWNT is 0.6-0.7 nm.

Thermal physics in carbon nanotube growth kinetics.

The growth of single wall carbon nanotubes (SWNTs) mediated by metal nanoparticles is considered within (i) the surface diffusion growth kinetics model coupled with (ii) a thermal model taking into account heat release of carbon adsorption-desorption on nanotube surface and carbon incorporation into the nanotube wall and (iii) carbon nanotube-inert gas collisional heat exchange. Numerical simulations performed together with analytical estimates reveal various temperature regimes occurring during SWNT growth. During the initial stage, which is characterized by SWNT lengths that are shorter than the surface diffusion length of carbon atoms adsorbed on the SWNT wall, the SWNT temperature remains constant and is significantly higher than that of the ambient gas. After this stage the SWNT temperature decreases towards that of gas and becomes nonuniformly distributed over the length of the SWNT. The rate of SWNT cooling depends on the SWNT-gas collisional energy transfer that, from molecular dynamics simulations, is seen to be efficient only in the SWNT radial direction. The decreasing SWNT temperature may lead to solidification of the catalytic metal nanoparticle terminating SWNT growth or triggering nucleation of a new carbon layer and growth of multiwall carbon nanotubes.

Computational studies of carbon nanotube-hydrocarbon bond strengths at nanotube ends: effect of link heteroatom and hydrocarbon structure.

Semiempirical and density functional electronic structure theory methods were used to study SWNT-X--R bond strengths, where the single-walled carbon nanotube (SWNT) had an armchair or zigzag structure, the link heteroatom X was O, N(H), or S and the hydrocarbon chain R was CH(2)CH(3), CH(OH)CH(3), CHCH(2), or CH(CF(3))CH(3). In all systems the hydrocarbon was bonded to the end of the nanotube. The SWNT-X--R bond (that is, the bond joining the link atom to the hydrocarbon) is more than 0.4 eV stronger for armchair than for zigzag nanotubes with the same diameters, irrespective of whether O, N, or S are used as link atoms or whether OH, C==C, or CF(3) groups are present in the hydrocarbon chain. This raises the possibility for selective manipulation of armchair/zigzag nanotubes using a variety of link atoms and hydrocarbon structures. The SWNT-O--CH(CF(3))CH(3) bond is weaker than the SWNT-O--CH(2)CH(3) bond (for both armchair and zigzag nanotubes), while inclusion of a double bond in the ethyl chain increases the bond strengths. Also, SWNT-S--CH(2)CH(3) and SWNT-N(H)--CH(2)CH(3) bonds are stronger than SWNT-O--CH(2)CH(3) bonds.

Fluorescence contrast and threshold limit: implications for photodynamic diagnosis of basal cell carcinoma.

This study was designed to evaluate what application time of delta-5-aminolaevulinic acid (ALA) results in highest contrast between tumour and normal skin, in the interval 1-4 h, when using photodynamic diagnosis (PDD) of basal cell carcinomas (BCC) located on the face. Moreover, a value of the demarcation limit has been derived based on the fluorescence variation in normal skin adjacent to the tumour. Forty patients were included in the study, randomly allocated to four different groups with varying ALA application time in the range 1-4 h. The contrast, defined as the ratio between the fluorescence intensity in ALA-treated tumour tissue and normal skin, was calculated for each patient, and the mean values in each group were evaluated as a function of ALA application time. In addition, the fluorescence intensity variation in ALA-treated normal skin adjacent to the tumour was assessed. The results from this study show a peak of the mean contrast values after 3 h ALA application, but due to large interpatient variation, the mean contrast did not differ significantly in the interval 2-4 h. After 2 h ALA application, the fluorescence intensity variation in the normal ALA-treated skin was found to be at a maximum, which suggests that 2 h ALA application is not preferable when using PDD. Based on data of the fluorescence variation in ALA-treated normal skin after 3 and 4 h ALA application, a tolerance interval was calculated implying that values above 1.4 times the mean normal fluorescence indicate an abnormal condition. This tolerance limit agrees well with results obtained in a former study.