Understanding the determinants of stability and folding of small globular proteins from their energetics

The results of minimal model calculations suggest that the stability and the kinetic accessibility of the native state of small globular proteins are controlled by few "hot" sites. By mean of molecular dynamics simulations around the native conformation, which simulate the protein and the surrounding solvent at full--atom level, we generate an energetic map of the equilibrium state of the protein and simplify it with an Eigenvalue decomposition. The components of the Eigenvector associated with the lowest Eigenvalue indicate which are the "hot" sites responsible for the stability and for the fast folding of the protein. Comparison of these predictions with the results of mutatgenesis experiments, performed for five small proteins, provide an excellent agreement

Correlated Binomial Models and Correlation Structures

We discuss a general method to construct correlated binomial distributions by imposing several consistent relations on the joint probability function. We obtain self-consistency relations for the conditional correlations and conditional probabilities. The beta-binomial distribution is derived by a strong symmetric assumption on the conditional correlations. Our derivation clarifies the 'correlation' structure of the beta-binomial distribution. It is also possible to study the correlation structures of other probability distributions of exchangeable (homogeneous) correlated Bernoulli random variables. We study some distribution functions and discuss their behaviors in terms of their correlation structures.Comment: 12 pages, 7 figure

Pyramiding resistance genes and widening the genetic base of the apple (Malus 7 domestica Borkh.) crop

Apple breeding is active worldwide and yet the apple crop is in a precarious state as it relies on few dominant cultivars and only the Rvi6 (formerly Vf) gene, that confers resistance to scab, has been extensively exploited in the cultivars entered the market in recent years. However, there are some 20 disease resistance genes described in apple and the apple germplasm includes thousands of accessions in the repositories. In this paper, a breeding programme is described, whereby 36 genotypes, including ancient and contemporary apple cultivars, were crossed to produce a new set of selections that combine extensive genetic resources with pyramided resistance genes to several apple diseases, such as scab and powdery mildew. The 110 cross combinations carried out successfully, of the 260 initially planned, produced 7,876 offsprings, reduced to 2,969 after screening with molecular markers associated with five resistance genes. Selections with three or two resistance genes and good agronomic characteristics were kept for further field observations with the aims of creating new cultivars for the market and new parents for future breeding projects

Influence of conformational fluctuations on enzymatic activity: modelling the functional motion of beta-secretase

Considerable insight into the functional activity of proteins and enzymes can be obtained by studying the low-energy conformational distortions that the biopolymer can sustain. We carry out the characterization of these large scale structural changes for a protein of considerable pharmaceutical interest, the human $\beta$-secretase. Starting from the crystallographic structure of the protein, we use the recently introduced beta-Gaussian model to identify, with negligible computational expenditure, the most significant distortion occurring in thermal equilibrium and the associated time scales. The application of this strategy allows to gain considerable insight into the putative functional movements and, furthermore, helps to identify a handful of key regions in the protein which have an important mechanical influence on the enzymatic activity despite being spatially distant from the active site. The results obtained within the Gaussian model are validated through an extensive comparison against an all-atom Molecular Dynamics simulation.Comment: To be published in a special issue of J. Phys.: Cond. Mat. (Bedlewo Workshop

Targeted mutagenesis of the female-suppressor sygi gene in tetraploid kiwifruit by crispr/cas9

Kiwifruit belong to the genus Actinidia with 54 species apparently all functionally dioecious. The sex-determinants of the type XX/XY, with male heterogametic, operate independently of the ploidy level. Recently, the SyGI protein has been described as the suppressor of female development. In the present study, we exploited the CRISPR/Cas9 technology by targeting two different sites in the SyGI gene in order to induce a stable gene knock-out in two tetraploid male accessions of Actinidia chinensis var. chinensis. The two genotypes showed a regenerative efficiency of 58% and 73%, respectively. Despite not yet being able to verify the phenotypic effects on the flower structure, due to the long time required by tissue-cultured kiwifruit plants to flower, we obtained two regenerated lines showing near fixation of a unique modification in their genome, resulting in both cases in the onset of a premature stop codon, which induces the putative gene knock-out. Evaluation of gRNA1 locus for both regenerated plantlets resulted in co-amplification of a minor variant differing from the target region for a single nucleotide. A genomic duplication of the region in proximity of the Y genomic region could be postulated

Are universities responding to the needs of students from refugee backgrounds?

Although many Australian universities have been proactive in responding to students' diverse needs through orientation and support programs, very little is known about programs needed for the successful transition of students from refugee backgrounds into tertiary study. Facilitating the early engagement of students with their studies and campus life is linked to greater student satisfaction, improved retention rates and better educational outcomes. One of the challenges that academics face is the paucity of research on the learning styles and academic needs of African and Middle Eastern students from refugee backgrounds.This paper reports on a needs analysis undertaken with a group of students from refugee backgrounds in Victoria and Western Australia, using in-depth interviews and focus group discussions. Participants reported that current support systems and programs are inadequate or non-existent and that many feel disadvantaged compared to Australian-born and international students. The article concludes with recommendations on how universities can better respond to the needs of students from refugee backgrounds

Poisson-Bracket Approach to the Dynamics of Nematic Liquid Crystals. The Role of Spin Angular Momentum

Nematic liquid crystals are well modeled as a fluid of rigid rods. Starting from this model, we use a Poisson-bracket formalism to derive the equations governing the dynamics of nematic liquid crystals. We treat the spin angular momentum density arising from the rotation of constituent molecules about their centers of mass as an independent field and derive equations for it, the mass density, the momentum density, and the nematic director. Our equations reduce to the original Leslie-Ericksen equations, including the inertial director term that is neglected in the hydrodynamic limit, only when the moment of inertia for angular momentum parallel to the director vanishes and when a dissipative coefficient favoring locking of the angular frequencies of director rotation and spin angular momentum diverges. Our equations reduce to the equations of nematohydrodynamics in the hydrodynamic limit but with dissipative coefficients that depend on the coefficient that must diverge to produce the Leslie-Ericksen equations.Comment: 10 pages, to be published in Phys. Rev. E 72(5

Avaliação dos impactos econômicos, sociais e ambientais de tecnologias geradas pela Embrapa Trigo - ano base 2007.

bitstream/CNPT-2010/40714/1/p-do96.pd