Identification and Validation of EST-Derived Molecular Markers, TRAP and VNTRs, for Banana Research

The advent of high-throughput sequencing technology has generated abundant information on DNA sequences for the genomes of many plant species. Expressed Sequence Tags (ESTs), which are unique DNA sequences derived from a cDNA library and therefore representing genes transcribed in specific tissues or at some stage of development, are one type of DNA sequences highly available today for many important crop species. Molecular markers are used for bridging DNA sequence information with particular phenotypes and are useful tools for genotyping germplasm collections and also for tagging genes involved in desirable agronomic traits. In this sense, there is always a strong demand for suitable marker techniques to better utilise existing sequence information. A transcriptome database from banana (Musa spp.), DATAMusa, containing 42,724 ESTs from 11 different cDNA libraries and encompassing approximately 24 Mb of DNA sequence, was used in this study for the design of primers to PCR-amplify two types of EST-derived molecular markers, Variable Nucleotide Tandem Repeat (VNTR) and Target Region Amplification Polymorphism (TRAP). These primers were then validated against a panel of 14 diploid Musa genotypes and produced 32 (VNTR) and 119 (TRAP) alleles. Used separately or together, both types of markers were able to discriminate Musa genotypes from different genome background (A or B genomes). The TRAP alleles identified were derived from only one EST, while the VNTR alleles were derived from 12 unigenes. Based on the results of this study, EST-derived markers can be an important source of polymorphism to be used in genetic diversity and gene discovery studies in banan

Variable number of tandem repeat markers in the genome sequence of Mycosphaerella fijiensis, the causal agent of black leaf streak disease of banana (Musa spp)

ABSTRACT. We searched the genome of Mycosphaerella fijiensis for molecular markers that would allow population genetics analysis of this plant pathogen. M. fijiensis, the causal agent of banana leaf streak disease, also known as black Sigatoka, is the most devastating pathogen attacking bananas (Musa spp). Recently, the entire genome sequence of M. fijiensis became available. We screened this database for VNTR markers. Forty-two primer pairs were selected for validation, based on repeat type and length and the number of repeat units. Five VNTR markers showing multiple alleles were validated with a reference set of isolates from different parts of the world and a population from a banana plantation in Costa Rica. Polymorphism information content values varied from 0.6414 to 0.7544 for the reference set and from 0.0400 and 0.7373 for the population set. Eighty percent of the polymorphism information content values were above 0.60, indicating that the markers are highly informative. These markers allowed robust scoring of agarose gels and proved to be useful for variability and population genetics studies. In conclusion, the strategy we developed to identify and validate VNTR markers is an efficient means to incorporate markers that can be used for fungicide resistance management and to develop breeding strategies to control banana black leaf streak disease. This is the first report of VNTR-minisatellites from the M. fijiensis genome sequence. Key words: Molecular markers; VNTRs; Genetic diversity; Population genetics; Black Sigatok

Correlation effects and the high-frequency spin susceptibility of an electron liquid: Exact limits

Spin correlations in an interacting electron liquid are studied in the high-frequency limit and in both two and three dimensions. The third-moment sum rule is evaluated and used to derive exact limiting forms (at both long- and short-wavelengths) for the spin-antisymmetric local-field factor, $\lim_{\omega \to \infty}G_-({\bf q, \omega})$. In two dimensions $\lim_{\omega \to \infty}G_-({\bf q, \omega})$ is found to diverge as $1/q$ at long wavelengths, and the spin-antisymmetric exchange-correlation kernel of time-dependent spin density functional theory diverges as $1/q^2$ in both two and three dimensions. These signal a failure of the local-density approximation, one that can be redressed by alternative approaches.Comment: 5 page

From semiclassical transport to quantum Hall effect under low-field Landau quantization

The crossover from the semiclassical transport to quantum Hall effect is studied by examining a two-dimensional electron system in an AlGaAs/GaAs heterostructure. By probing the magneto-oscillations, it is shown that the semiclassical Shubnikov-de Haas (SdH) formulation can be valid even when the minima of the longitudinal resistivity approach zero. The extension of the applicable range of the SdH theory could be due to the damping effects resulting from disorder and temperature. Moreover, we observed plateau-plateau transition like behavior with such an extension. From our study, it is important to include the positive magnetoresistance to refine the SdH theory.Comment: 11 pages, 5 figure

Supersymmetric Intersecting Branes on the Type IIA T^6/Z_4 orientifold

We study supersymmetric intersecting D6-branes wrapping 3-cycles in the Type IIA T^6/Z_4 orientifold background. As a new feature, the 3-cycles in this orbifold space arise both from the untwisted and the Z_2 twisted sectors. We present an integral basis for the homology lattice, H_3(M,Z), in terms of fractional 3-cycles, for which the intersection form involves the Cartan matrix of E8. We show that these fractional D6-branes can be used to construct supersymmetric brane configurations realizing a three generation Pati-Salam model. Via brane recombination processes preserving supersymmetry, this GUT model can be broken down to a standard-like model.Comment: 48 pages, TeX, harvmac, 8 figures, v4: some signs correcte

The effect of feeder system and diet on welfare, performance and meat quality, of growing-finishing Iberian × Duroc pigs under high environmental temperatures

The present study investigated the replacement of 5% of starch (ST) by 5% of sunflower oil (SO), with or without feed restriction, in the diet of growing-finishing Iberian × Duroc pigs exposed to heat stress conditions. The effects of these strategies on the welfare, performance and meat quality of the animals were evaluated. Seventy-two crossbred males [51.00 ± 6.29 kg body weight (BW)] were housed in collective pens and randomly distributed according to their initial BW in climate-controlled rooms under heat stress conditions (30–32 °C; 35%–50% humidity). The experiment was carried out in a randomized block design, in a 2 × 2 factorial design composed of two diets (control or oil) and two feed management (ad-libitum and restriction) types. The investigated treatments were: 1) control diet (5% ST × 0% SO) with ad-libitum feed intake, 2) oil diet (replacement of 5% of ST by 5% SO) with ad-libitum feed intake, 3) control diet with restriction feed intake, and 4) oil diet with restriction feed intake. The pigs’ behavior and dirtiness score were observed daily, and their performance was assessed weekly. Furthermore, three blood samples were collected from each animal for hemogram analysis during the period of study. The analysis of meat and carcass quality was performed 24 h post-mortem once the animals had reached an average BW of 130–140 kg. Statistical analyses were performed using the PROC MIXED and PROC GENMOD procedures of the Statistical Analysis System (SAS). The diet-regimen interaction produced no effects (P > 0.05) on the analyzed variables, except for behavior. Animals on the control diet associated with ad-libitum feed management spent more time in the lateral decubitus position and showed reduced activity. In addition, pigs fed ad-libitum and those that received the control diet displayed the highest level of dirtiness during the experiment. Evaluation of performance revealed that pigs receiving the oil diet showed reduced feed intake (P < 0.05) with no difference in average daily gain and consequently presented better feed conversion values compared to animals on the control diet. Furthermore, the oil diet resulted in a higher (P < 0.05) carcass yield as well as a higher oleic fat content in the meat. Pigs on restricted feeding management with lower body and carcass weights produced higher values of leanness percentage and carcass compared to animals in the ad-libitum group. In conclusion, the replacement of 5% of starch by 5% of sunflower oil in the pigs’ diet during high ambient temperatures improved the animals’ welfare, feed efficiency, and carcass characteristics.info:eu-repo/semantics/acceptedVersio

Highly Endemic, Waterborne Toxoplasmosis in North Rio de Janeiro State, Brazil

In Campos dos Goytacazes, northern Rio de Janeiro state, Brazil, reports of uveitis consistent with toxoplasmosis led to a survey of the prevalence and risk factors for Toxoplasma gondii infection in 1997–1999. The survey population was selected randomly from schools, randomly chosen communities, and an army battalion. Serum samples from 1,436 persons were tested. With results adjusted for age, 84% of the population in the lower socioeconomic group was seropositive, compared with 62% and 23% of the middle and upper socioeconomic groups, respectively (p<0.001). When multivariate analysis was performed, drinking unfiltered water was found to increase the risk of seropositivity for the lower socioeconomic (odds ratio [OR]: 3.0, 95% confidence interval [CI] 1.3 to 6.9) and middle socioeconomic (OR: 1.7, 95% CI 1.2 to 2.3) populations. We also found a high T. gondii seroprevalence in this Brazilian community. Drinking unfiltered water increased the risk of T. gondii seropositivity, indicating the potential importance of oocyst transmission in water in this region

Factorizing the hard and soft spectator scattering contributions for the nucleon form factor F_1 at large Q^2

We investigate the soft spectator scattering contribution for the FF $F_{1}$. We focus our attention on factorization of the hard-collinear scale $\sim Q\Lambda$ corresponding to transition from SCET-I to SCET-II. We compute the leading order jet functions and find that the convolution integrals over the soft fractions are logarithmically divergent. This divergency is the consequence of the boost invariance and does not depend on the model of the soft correlation function describing the soft spectator quarks. Using as example a two-loop diagram we demonstrated that such a divergency corresponds to the overlap of the soft and collinear regions. As a result one obtains large rapidity logarithm which must be included in the correct factorization formalism. We conclude that a consistent description of the factorization for $F_{1}$ implies the end-point collinear divergencies in the hard and soft spectator contributions, i.e. convolution integrals with respect to collinear fractions are not well-defined. Such scenario can only be realized when the twist-3 nucleon distribution amplitude has specific end-point behavior which differs from one expected from the evolution of the nucleon distribution amplitude. Such behavior leads to the violation of the collinear factorization for the hard spectator scattering contribution. We suggest that the soft spectator scattering and chiral symmetry breaking provide the mechanism responsible for the violation of collinear factorization in case of form factor $F_{1}$.Comment: 25 pages, 6 figures, text is improved, few typos corrected, one figure added, statement about end-point behavior of the nucleon DA is formulated more accuratel

Specific patterns of brain alterations underlie distinct clinical profiles in Huntington's disease

Huntington's disease (HD) is a genetic neurodegenerative disease which involves a triad of motor, cognitive and psychiatric disturbances. However, there is great variability in the prominence of each type of symptom across individuals. The neurobiological basis of such variability remains poorly understood but would be crucial for better tailored treatments. Multivariate multimodal neuroimaging approaches have been successful in disentangling these profiles in other disorders. Thus we applied for the first time such approach to HD. We studied the relationship between HD symptom domains and multimodal measures sensitive to grey and white matter structural alterations. Forty-three HD gene carriers (23 manifest and 20 premanifest individuals) were scanned and underwent behavioural assessments evaluating motor, cognitive and psychiatric domains. We conducted a multimodal analysis integrating different structural neuroimaging modalities measuring grey matter volume, cortical thickness and white matter diffusion indices - fractional anisotropy and radial diffusivity. All neuroimaging measures were entered into a linked independent component analysis in order to obtain multimodal components reflecting common inter-subject variation across imaging modalities. The relationship between multimodal neuroimaging independent components and behavioural measures was analysed using multiple linear regression. We found that cognitive and motor symptoms shared a common neurobiological basis, whereas the psychiatric domain presented a differentiated neural signature. Behavioural measures of different symptom domains correlated with different neuroimaging components, both the brain regions involved and the neuroimaging modalities most prominently associated with each type of symptom showing differences. More severe cognitive and motor signs together were associated with a multimodal component consisting in a pattern of reduced grey matter, cortical thickness and white matter integrity in cognitive and motor related networks. In contrast, depressive symptoms were associated with a component mainly characterised by reduced cortical thickness pattern in limbic and paralimbic regions. In conclusion, using a multivariate multimodal approach we were able to disentangle the neurobiological substrates of two distinct symptom profiles in HD: one characterised by cognitive and motor features dissociated from a psychiatric profile. These results open a new view on a disease classically considered as a uniform entity and initiates a new avenue for further research considering these qualitative individual differences

A Quantitative Model of Energy Release and Heating by Time-dependent, Localized Reconnection in a Flare with a Thermal Loop-top X-ray Source

We present a quantitative model of the magnetic energy stored and then released through magnetic reconnection for a flare on 26 Feb 2004. This flare, well observed by RHESSI and TRACE, shows evidence of non-thermal electrons only for a brief, early phase. Throughout the main period of energy release there is a super-hot (T>30 MK) plasma emitting thermal bremsstrahlung atop the flare loops. Our model describes the heating and compression of such a source by localized, transient magnetic reconnection. It is a three-dimensional generalization of the Petschek model whereby Alfven-speed retraction following reconnection drives supersonic inflows parallel to the field lines, which form shocks heating, compressing, and confining a loop-top plasma plug. The confining inflows provide longer life than a freely-expanding or conductively-cooling plasma of similar size and temperature. Superposition of successive transient episodes of localized reconnection across a current sheet produces an apparently persistent, localized source of high-temperature emission. The temperature of the source decreases smoothly on a time scale consistent with observations, far longer than the cooling time of a single plug. Built from a disordered collection of small plugs, the source need not have the coherent jet-like structure predicted by steady-state reconnection models. This new model predicts temperatures and emission measure consistent with the observations of 26 Feb 2004. Furthermore, the total energy released by the flare is found to be roughly consistent with that predicted by the model. Only a small fraction of the energy released appears in the super-hot source at any one time, but roughly a quarter of the flare energy is thermalized by the reconnection shocks over the course of the flare. All energy is presumed to ultimately appear in the lower-temperature T<20 MK, post-flare loops