10,005 research outputs found
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 -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
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