Discrimination of Shark species by simple PCR of 5S rDNA repeats

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

A simple graphical model of small mammal succession after fire in the Brazilian cerrado

We studied the succession of small mammal species after fire in the cerrado (Neotropical savanna) of Central Brazil. Populations of small mammals were sampled with live-trapping techniques in a series of nine sites of different successional age, ranging from 1 to 26 years after fire. Ten species of small mammals were captured through all the seral stages of succession. Species richness ranged from two to seven species by seral stage. The species were arranged in different groups with respect to abundance along the succession: the first was composed of early successional species that peaked <2 years after fire (Calomys callosus, C. tener, Thalpomys cerradensis, Mus musculus, Thylamys velutinus); the second occurred or peaked 2-3 years after fire (Necromys lasiurus, Gracilinanus sp., Oryzomys scoth). Gracilinanus agilis peaked in the last seral stage. Species richness of small mammals showed an abrupt decrease from an average of four species immediately after fire to two species 5-26 years after the last fire. We propose a simple graphical model to explain the pattern of species richness of small mammals after fire in the cerrado. This model assumes that the occurrence of species of small mammals is determined by habitat selection behavior by each species along a habitat gradient. The habitat gradient is defined as the ratio of cover of herbaceous to woody vegetation. The replacement of species results from a trade-off in habitat requirements for the two habitat variables.

A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements

We report a method for studying global DNA methylation based on using bisulfite treatment of DNA and simultaneous PCR of multiple DNA repetitive elements, such as Alu elements and long interspersed nucleotide elements (LINE). The PCR product, which represents a pool of approximately 15000 genomic loci, could be used for direct sequencing, selective restriction digestion or pyrosequencing, in order to quantitate DNA methylation. By restriction digestion or pyrosequencing, the assay was reproducible with a standard deviation of only 2% between assays. Using this method we found that almost two-thirds of the CpG methylation sites in Alu elements are mutated, but of the remaining methylation target sites, 87% were methylated. Due to the heavy methylation of repetitive elements, this assay was especially useful in detecting decreases in DNA methylation, and this assay was validated by examining cell lines treated with the methylation inhibitor 5-aza-2'deoxycytidine (DAC), where we found a 1-16% decrease in Alu element and 18-60% LINE methylation within 3 days of treatment. This method can be used as a surrogate marker of genome-wide methylation changes. In addition, it is less labor intensive and requires less DNA than previous methods of assessing global DNA methylation.

A simple procedure for rehybridization of nuclei analyzed previously by fish

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Gaussian quadrature rules with simple node-weight relations

In this paper, we consider the symmetric Gaussian and L-Gaussian quadrature rules associated with twin periodic recurrence relations with possible variations in the initial coefficient. We show that the weights of the associated Gaussian quadrature rules can be given as rational functions in terms of the corresponding nodes where the numerators and denominators are polynomials of degree at most 4. We also show that the weights of the associated L-Gaussian quadrature rules can be given as rational functions in terms of the corresponding nodes where the numerators and denominators are polynomials of degree at most 5. Special cases of these quadrature rules are given. Finally, an easy to implement procedure for the evaluation of the nodes is described.

Stability of breathers in simple mechanical models for DNA

This work studies through the Floquet theory the stability of breathers generated by the anti-continuous limit. We used the Peyrard-Bishop model for DNA and two kinds of nonlinear potential: the Morse potential and a potential with a hump. The comparison of their stability was done in function of the coupling parameter. We also investigate the dynamic behaviour of the system in stable and unstable regions. Qualitatively, the dynamic of mobile breathers resembles DNA.

Water quality index as a simple indicator of aquaculture effects on aquatic bodies

This paper proposes a water quality index (WQI) to subsidize management actions in the Medio Paranapanema Watershed in São Paulo State, Brazil, as a simple pollution indicator for aquaculture activity. Water quality of the Macuco and Queixada rivers was investigated for 2 years (from May 2003 to May 2005). The index proposed in this work is composed of three measurable environmental parameters-turbidity, total phosphorus and dissolved oxygen. Concentrations of these three variables were normalized on a scale from 0 to 100 and translated into statements of water quality (excellent, good, regular, fair and poor). The index was applied to seventeen monitoring points in the aquatic bodies described above and compared to others, one being that used by the Environmental Protection Agency of United States and proposed for the National Sanitation Foundation, other employing minimal index and the last one considering the minimum operator concept. The results show that the degradation in this watershed from aquaculture activity can be easily inferred with this index, which is more restricted than the others routinely used to infer water quality. (C) 2007 Elsevier Ltd. All rights reserved.

Development of a simple and versatile ultrafiltration system for the fractionation of aquatic humic substances

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Cosmic microwave background and large-scale structure constraints on a simple quintessential inflation model

We derive constraints on a simple quintessential inflation model, based on a spontaneously broken Phi(4) theory, imposed by the Wilkinson Microwave Anisotropy Probe three-year data (WMAP3) and by galaxy clustering results from the Sloan Digital Sky Survey (SDSS). We find that the scale of symmetry breaking must be larger than about 3 Planck masses in order for inflation to generate acceptable values of the scalar spectral index and of the tensor-to-scalar ratio. We also show that the resulting quintessence equation of state can evolve rapidly at recent times and hence can potentially be distinguished from a simple cosmological constant in this parameter regime.

Light-cone gauge integrals: prescriptionlessness at two loops

The only calculations performed beyond one-loop level in the light-cone gauge make use of the Mandelstam-Leibbrandt (ML) prescription in order to circumvent the notorious gauge dependent poles. Recently we have shown that in the context of negative dimensional integration method (NDIM) such prescription can be altogether abandoned, at least in one-loop order calculations. We extend our approach, now studying two-loop integrals pertaining to two-point functions. While previous works on the subject present only divergent parts for the integrals, we show that our prescriptionless method gives the same results for them, besides finite parts for arbitrary exponents of propagators. (C) 2000 Elsevier B.V. B.V. All rights reserved.

Chiral corrections to baryon properties with composite pions

A calculational scheme is developed to evaluate chiral corrections to properties of composite baryons with composite pions. The composite baryons and pions are bound states derived from a microscopic chiral quark model. The model is amenable to standard many-body techniques such as the BCS and random phase approximation formalisms. An effective chiral model involving only hadronic degrees of freedom is derived from the macroscopic quark model by projection onto hadron states. Chiral loops are calculated using the effective hadronic Hamiltonian. A simple microscopic confining interaction is used to illustrate the derivation of the pion-nucleon form factor and the calculation of picnic self-energy corrections to the nucleon and Delta (1232) masses.

Simple derivation of general Fierz-type identities

General Fierz-type identities are examined and their well-known connection with completeness relations in matrix vector spaces is shown. In particular, I derive the chiral Fierz identities in a simple and systematic way by using a chiral basis for the complex 4 X 4 matrices. Other completeness relations for the fundamental representations of SU(N) algebras can be extracted using the same reasoning. (c) 2005 American Association of Physics Teachers.

Dressed-state approach to a simple radiating atom

We consider a system consisting of an atom in the dipole approximation, coupled to the electromagnetic field. Using recently introduced renormalized coordinates and dressed states, we give a non-perturbative solution to the atom radiation process. From this formalism a non-exponential decay law naturally emerges. However, at least for low frequencies and weak coupling, there is only a very small, practically non-detectable, deviation from a purely exponential decay, in agreement with all previous results in the literature. (c) 2005 Elsevier B.V. All rights reserved.

Dual superconformal symmetry, and the amplitude/Wilson loop connection

We show that tree level superstring theories on certain supersymmetric backgrounds admit a symmetry which we call "fermionic T-duality". This is a non-local redefinition of the fermionic worldsheet fields similar to the redefinition we perform on bosonic variables when we do an ordinary T-duality. This duality maps a supersymmetric background to another supersymmetric background with different RR fields and a different dilaton. We show that a certain combination of bosonic and fermionic T-dualities maps the full superstring theory on AdS(5) x S-5 back to itself in such a way that gluon scattering amplitudes in the original theory map to something very close to Wilson loops in the dual theory. This duality maps the "dual superconformal symmetry" of the original theory to the ordinary superconformal symmetry of the dual model. This explains the dual superconformal invariance of planar scattering amplitudes of N = 4 super Yang Mills and also sheds some light on the connection between amplitudes and Wilson loops. In the appendix, we propose a simple prescription for open superstring MHV tree amplitudes in a flat background.

Two-Point Function at Two Loops via Triangle Diagram Insertion

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)