Microscopic description of the twist mode in normal and superfluid trapped Fermi gases

We investigate the "twist" mode (rotation of the upper against the lower hemisphere) of a dilute atomic Fermi gas in a spherical trap. The normal and superfluid phases are considered. The linear response to this external perturbation is calculated within the microscopic Hartree-Fock-Bogoliubov approach. In the normal phase the excitation spectrum is concentrated in a rather narrow peak very close to the trapping frequency. In the superfluid phase the strength starts to be damped and fragmented and the collectivity of the mode is progressively lost when the temperature decreases. In the weak-pairing regime some reminiscence of the collective motion still exists, whereas in the strong-pairing regime the twist mode is completely washed out. The disappearance of the twist mode in the strong-pairing regime with decreasing temperature is interpreted in the framework of the two-fluid model.

Temperature-induced resonances and Landau damping of collective modes in Bose-Einstein condensed gases in spherical traps

Interaction between collective monopole oscillations of a trapped Bose-Einstein condensate and thermal excitations is investigated by means of perturbation theory. We assume spherical symmetry to calculate the matrix elements by solving the linearized Gross-Pitaevskii equations. We use them to study the resonances of the condensate induced by temperature when an external perturbation of the trapping frequency is applied and to calculate the Landau damping of the oscillations.

First-passage-time noninteger moments for some diffusion and dichotomous processes

We calculate noninteger moments ¿tq¿ of first passage time to trapping, at both ends of an interval (0,L), for some diffusion and dichotomous processes. We find the critical behavior of ¿tq¿, as a function of q, for free processes. We also show that the addition of a potential can destroy criticality.

Meissner effect and critical fields in an inhomogeneous Ba2HoCu3O7-x high-Tc superconductor

The Meissner and diamagnetic shielding effects and the upper, lower, and thermodynamical critical fields have been studied in a Ba2HoCu3O7-x sample using magnetization measurements in fields up to 55 kOe. The diamagnetic shielding curve shows the existence of a transition at Tc=91.5 K followed by a broad transition extending from 85 to 25 K which may be related to inhomogeneities in the oxygen content of the sample. A rather low flux expulsion (13.5%) is observed which we attribute to flux pinning or trapping. We show that the coexistence of superconducting and nonsuperconducting regions within the sample at temperatures just below Tc leads to strong reductions in the critical magnetic fields.

Unexpected genomic variability in clinical and environmental strains of the pathogenic yeast Candida parapsilosis

Invasive candidiasis is the most commonly reported invasive fungal infection worldwide. Although Candida albicans remains the main cause, the incidence of emerging Candida species, such as C. parapsilosis is increasing. It has been postulated that C. parapsilosis clinical isolates result from a recent global expansion of a virulent clone. However, the availability of a single genome for this species has so far prevented testing this hypothesis at genomic scales. We present here the sequence of three additional strains from clinical and environmental samples. Our analyses reveal unexpected patterns of genomic variation, shared among distant strains, that argue against the clonal expansion hypothesis. All strains carry independent expansions involving an arsenite transporter homolog, pointing to the existence of directional selection in the environment, and independent origins of the two clinical isolates. Furthermore, we report the first evidence for the existence of recombination in this species. Altogether, our results shed new light onto the dynamics of genome evolution in C. parapsilosis.

Review. Characterization and selection of hexaploid wheats containing resistance to Heterodera avenae or Mayetiola destructor introgressed from Aegilops

Cereal cyst nematode (CCN, Heterodera avenae) and Hessian fly (HF, Mayetiola destructor) are two major pests affecting wheat crops worldwide including important cereal areas of Spain. Aegilops ventricosa and Ae. triuncialis were used as donors in a strategy to introduce resistance genes (RG) for these pests in hexaploid wheat (Triticum aestivum L.). Two 42 chromosomes introgression lines have been derived from Ae. ventricosa: H-93-8 and H-93-33 carrying genes Cre2 and H27 conferring resistance to CCN and HF, respectively. Line TR-3531 with 42 chromosomes has been derived from Ae. triuncialis and carries RGs conferring resistance for CCN (Cre7) and for HF (H30). Alien material has been incorporated in lines H-93 by chromosomal substitution and recombination, while in line TR-3531 homoeologous recombination affecting small DNA fragments has played a major role. It has been demonstrated that Cre2, Cre7, H27 and H30 are major single dominant genes and not allelic of other previously described RGs. Biochemical and molecular-biology studies of the defense mechanism triggered by Cre2 and Cre7 have revealed specific induction of peroxidase and other antioxidant enzymes. In parallel to these basic studies advanced lines carrying resistance genes for CNN and/or HF have been developed. Selection was done using molecular markers for eventually «pyramiding» resistance genes. Several isozyme and RAPD markers have been described and, currently, new markers based on transposable elements and NBS-LRR sequences are being developed. At present, two advanced lines have already been included at the Spanish Catalogue of Commercial Plant Varieties.

Gene flow and gene flux shape evolutionary patterns of variation in Drosophila subobscura

Gene flow (defined as allele exchange between populations) and gene flux (defined as allele exchange during meiosis in heterokaryotypic females) are important factors decreasing genetic differentiation between populations and inversions. Many chromosomal inversions are under strong selection and their role in recombination reduction enhances the maintenance of their genetic distinctness. Here we analyze levels and patterns of nucleotide diversity, selection and demographic history, using 37 individuals of Drosophila subobscura from Mount Parnes (Greece) and Barcelona (Spain). Our sampling focused on two frequent O-chromosome arrangements that differ by two overlapping inversions (OST and O3+4), which are differentially adapted to the environment as observed by their opposing latitudinal clines in inversion frequencies. The six analyzed genes (Pif1A, Abi, Sqd, Yrt, Atpa and Fmr1) were selected for their location across the O-chromosome and their implication in thermal adaptation. Despite the extensive gene flux detected outside the inverted region, significant genetic differentiation between both arrangements was found inside it. However, high levels of gene flow were detected for all six genes when comparing the same arrangement among populations. These results suggest that the adaptive value of inversions is maintained, regardless of the lack of genetic differentiation within arrangements from different populations, and thus favors the Local Adaptation hypothesis over the Coadapted Genome hypothesis as the basis of the selection acting on inversions in these populations.

Structural factors impacting carrier transport and electroluminescence from Si nanocluster-sensitized Er ions.

We present an analysis of factors influencing carrier transport and electroluminescence (EL) at 1.5 µm from erbium-doped silicon-rich silica (SiOx) layers. The effects of both the active layer thickness and the Si excess content on the electrical excitation of erbium are studied. We demonstrate that when the thickness is decreased from a few hundred to tens of nanometers the conductivity is greatly enhanced. Carrier transport is well described in all cases by a Poole-Frenkel mechanism, while the thickness-dependent current density suggests an evolution of both density and distribution of trapping states induced by Si nanoinclusions. We ascribe this observation to stress-induced effects prevailing in thin films, which inhibit the agglomeration of Si atoms, resulting in a high density of sub-nm Si inclusions that induce traps much shallower than those generated by Si nanoclusters (Si-ncs) formed in thicker films. There is no direct correlation between high conductivity and optimized EL intensity at 1.5 µm. Our results suggest that the main excitation mechanism governing the EL signal is impact excitation, which gradually becomes more efficient as film thickness increases, thanks to the increased segregation of Si-ncs, which in turn allows more efficient injection of hot electrons into the oxide matrix. Optimization of the EL signal is thus found to be a compromise between conductivity and both number and degree of segregation of Si-ncs, all of which are governed by a combination of excess Si content and sample thickness. This material study has strong implications for many electrically driven devices using Si-ncs or Si-excess mediated EL.

Surface passivation of crystalline silicon by Cat-CVD amorphous and nanocrystalline thin silicon films

In this work, we study the electronic surface passivation of crystalline silicon with intrinsic thin silicon films deposited by Catalytic CVD. The contactless method used to determine the effective surface recombination velocity was the quasi-steady-state photoconductance technique. Hydrogenated amorphous and nanocrystalline silicon films were evaluated as passivating layers on n- and p-type float zone silicon wafers. The best results were obtained with amorphous silicon films, which allowed effective surface recombination velocities as low as 60 and 130 cms -1 on p- and n-type silicon, respectively. To our knowledge, these are the best results ever reported with intrinsic amorphous silicon films deposited by Catalytic CVD. The passivating properties of nanocrystalline silicon films strongly depended on the deposition conditions, especially on the filament temperature. Samples grown at lower filament temperatures (1600 °C) allowed effective surface recombination velocities of 450 and 600 cms -1 on n- and p-type silicon.

Allelic diversity and population structure in Vibrio cholerae O139 Bengal based on nucleotide sequence analysis

Comparative analysis of gene fragments of six housekeeping loci, distributed around the two chromosomes of Vibrio cholerae, has been carried out for a collection of 29 V. cholerae O139 Bengal strains isolated from India during the first epidemic period (1992 to 1993). A toxigenic O1 ElTor strain from the seventh pandemic and an environmental non-O1/non-O139 strain were also included in this study. All loci studied were polymorphic, with a small number of polymorphic sites in the sequenced fragments. The genetic diversity determined for our O139 population is concordant with a previous multilocus enzyme electrophoresis study in which we analyzed the same V. cholerae O139 strains. In both studies we have found a higher genetic diversity than reported previously in other molecular studies. The results of the present work showed that O139 strains clustered in several lineages of the dendrogram generated from the matrix of allelic mismatches between the different genotypes, a finding which does not support the hypothesis previously reported that the O139 serogroup is a unique clone. The statistical analysis performed in the V. cholerae O139 isolates suggested a clonal population structure. Moreover, the application of the Sawyer's test and split decomposition to detect intragenic recombination in the sequenced gene fragments did not indicate the existence of recombination in our O139 population.

Understanding Optical Trapping Phenomena: a Simulation for Undergraduates

Optical trapping is an attractive and multidisciplinary topic that has become the center of attention to a large number of researchers. Moreover, it is a suitable subject for advanced students that requires a knowledge of a wide range of topics. As a result, it has been incorporated into some syllabuses of both undergraduate and graduate programs. In this paper, basic concepts in laser trapping theory are reviewed. To provide a better understanding of the underlying concepts for students, a Java application for simulating the behavior of a dielectric particle trapped in a highly focused beam has been developed. The program illustrates a wide range of theoretical results and features, such as the calculation of the force exerted by a beam in the Mie and Rayleigh regimes or the calibration of the trap stiffness. Some examples that are ready to be used in the classroom or in the computer lab are also supplied.

Optical trapping: a review of essential concepts

Optical tweezers are an innovative technique for the non-contact, all-optical manipulation of small material samples, which has extraordinarily expanded and evolved since its inception in the mid-80s of the last century. Nowadays, the potential of optical tweezers has been clearly proven and a wide range of applications both from the physical and biological sciences have solidly emerged, turning the early ideas and techniques into a powerful paradigm for experimentation in the micro- and nanoworld. This review aims at highlighting the fundamental concepts that are essential for a thorough understanding of optical trapping, making emphasis on both its manipulation and measurement capabilities, as well as on the vast array of important biological applications appeared in the last years.

A chromosomal insertion toolbox for promoter probing, mutant complementation and pathogenicity studies in Ralstonia solanacearum

We describe here the construction of a delivery system for stable and directed insertion of gene constructs in a permissive chromosomal site of the bacterial wilt pathogen Ralstonia solanacearum. The system consists of a collection of suicide vectors the Ralstonia chromosome (pRC) series that carry an integration element flanked by transcription terminators and two sequences of homology to the chromosome of strain GMI1000, where the integration element is inserted through a double recombination event. Unique restriction enzyme sites and a GATEWAY cassette enable cloning of any promoter::gene combination in the integration element. Variants endowed with different selectable antibiotic resistance genes and promoter::gene combinations are described. We show that the system can be readily used in GMI1000 and adapted to other R. solanacearum strains using an accessory plasmid. We prove that the pRC system can be employed to complement a deletion mutation with a single copy of the native gene, and to measure transcription of selected promoters in monocopy both in vitro and in planta. Finally, the system has been used to purify and study secretion type III effectors. These novel genetic tools will be particularly useful for the construction of recombinant bacteria that maintain inserted genes or reporter fusions in competitive situations (i.e., during plant infection).

Chromosomal polymorphism of D. subobscura: no differences between wild males and sons of wild females

When analyzing the chromosomal polymorphism of D. subobscura natural populations it is assumed that the information provided by wild males and sons of wild females is equivalent. Thus, using both in the analysis it is possible to increase the sample size. However, it is important to verify whether there are significant differences between both groups or not. The aim of this research has been to statistically compare the results of chromosomal polymorphism of both groups. We have used data from Avala Mountain (Serbia) where D. subobscura flies were collected from the 30th May to the 5th June 2011. Avala is located 18 km south of Belgrade and the trapping place is a forest with polydominant communities of Fagetum submontanum Table 1. Number and percentage of adult flies collected in Font Groga (Barcelona, Spain) on 9th October 2013. Males and sons of wild females were crossed with virgin females of the Küsnacht strain. Third instar larvae from F1 were dissected to obtain the salivary glands and the polytene chromosomes were stained and squashed in aceto-orcein solution. No significant differences were observed for any chromosome of the karyotype: A (p-value = 0.485), J (p-value = 0.230), U (p-value =0.572), E (p-value = 0.536), and O (p-value = 0.338). Thus, it seems that the two groups can be grouped together to obtain the chromosomal polymorphism of the population.