Mapping the transition state and pathway of protein folding by protein engineering

In the transition state for unfolding of barnase, the hydrophobic core between the major alpha-helix and beta-sheet is somewhat weakened, the C terminus of the major helix is largely intact but its N terminus is exposed and a major loop has been invaded by solvent.     

The new resonances Zcs(3985)and Zcs(4003)(almost)fill two tetraquark nonets of broken SU(3)f

Hadrons made by diquark-antidiquark pairs(tetraquarks)are held together by QCD forces in an overall color singlet.As stated in the original proposals and simila...     

A New Dimension Reduction Method: Factor Discriminant K-means

Reduced K-means (RKM) and Factorial K-means (FKM) are two data reduction techniques incorporating principal component analysis and K-means into a unified methodology to obtain a reduced set of components for variables and an optimal partition for objects. RKM finds clusters in a reduced space by maximizing the between-clusters deviance without imposing any condition on the within-clusters deviance, so that clusters are isolated but they might be heterogeneous. On the other hand, FKM identifies clusters in a reduced space by minimizing the within-clusters deviance without imposing any condition on the between-clusters deviance. Thus, clusters are homogeneous, but they might not be isolated. The two techniques give different results because the total deviance in the reduced space for the two methodologies is not constant; hence the minimization of the within-clusters deviance is not equivalent to the maximization of the between-clusters deviance. In this paper a modification of the two techniques is introduced to avoid the afore mentioned weaknesses. It is shown that the two modified methods give the same results, thus merging RKM and FKM into a new methodology. It is called Factor Discriminant K-means (FDKM), because it combines Linear Discriminant Analysis and K-means. The paper examines several theoretical properties of FDKM and its performances with a simulation study. An application on real-world data is presented to show the features of FDKM.     

Accurate Tree-based Missing Data Imputation and Data Fusion within the Statistical Learning Paradigm

Framework of this paper is statistical data editing, specifically how to edit or impute missing or contradictory data and how to merge two independent data sets presenting some lack of information. Assuming a missing at random mechanism, this paper provides an accurate tree-based methodology for both missing data imputation and data fusion that is justified within the Statistical Learning Theory of Vapnik. It considers both an incremental variable imputation method to improve computational efficiency as well as boosted trees to gain in prediction accuracy with respect to other methods. As a result, the best approximation of the structural risk (also known as irreducible error) is reached, thus reducing at minimum the generalization (or prediction) error of imputation. Moreover, it is distribution free, it holds independently of the underlying probability law generating missing data values. Performance analysis is discussed considering simulation case studies and real world applications.     

Increased migration of olfactory ensheathing cells secreting the Nogo receptor ectodomain over inhibitory substrates and lesioned spinal cord

Olfactory ensheathing cell (OEC) transplantation emerged some years ago as a promising therapeutic strategy to repair injured spinal cord. However, inhibitory molecules are present for long periods of time in lesioned spinal cord, inhibiting both OEC migration and axonal regrowth. Two families of these molecules, chondroitin sulphate proteoglycans (CSPG) and myelin-derived inhibitors (MAIs), are able to trigger inhibitory responses in lesioned axons. Mounting evidence suggests that OEC migration is inhibited by myelin. Here we demonstrate that OEC migration is largely inhibited by CSPGs and that inhibition can be overcome by the bacterial enzyme Chondroitinase ABC. In parallel, we have generated a stable OEC cell line overexpressing the Nogo receptor (NgR) ectodomain to reduce MAI-associated inhibition in vitro and in vivo. Results indicate that engineered cells migrate longer distances than unmodified OECs over myelin or oligodendrocyte-myelin glycoprotein (OMgp)-coated substrates. In addition, they also show improved migration in lesioned spinal cord. Our results provide new insights toward the improvement of the mechanisms of action and optimization of OEC-based cell therapy for spinal cord lesion.     

A chromosome study ofScarites occidentalis (Coleoptera,Caraboidea)

Summary Scarites occidentalis has 2n=41 (females 2n=42), n=19+X₁X₂Y. This multiple sex-chromosome system and other karyotypic characteristics suggest that this species andS. buparius share a recent common ancestor in which the sex trivalent was probably originated.Thanks are due to Dr N. Virkki for his valuable comments and his help with the English, to Dr Ramos and Dr Aparicio for discussion and advice, to Dr F. Hiraldo and M. Mañez for collecting the specimens. This work has been supported by a postdoctoral fellowship of the Consejo Superior de Investigaciones Científicas.     

Effect of alanine versus glycine in alpha-helices on protein stability.

The rational design of proteins requires knowledge of the helix-forming propensities (s-values) of the different amino acids. There is, however, considerable controversy about the relative values for alanine and glycine. We find from experiments on mutants of barnase that the relative effect of Ala versus Gly on helix stability depends crucially on the position in the helix (whether they are at the ends (caps) or are internal) and the context (the influence of their neighbours). Glycine is greatly preferred at the N and C caps. At internal positions, Ala stabilizes the helix relative to Gly by 0.4 to 2 kcal mol-1. The variation results from a combination of burial of hydrophobic surface on folding and interference with hydrogen bonding of the protein with solvent. There is a good empirical correlation between the relative stabilizing effects of Ala and Gly with the total change in solvent-accessible hydrophobic surface area of the folded protein on mutation of Gly to Ala. It is not valid to assign to each amino acid a unique s-value that is generally applicable to all positions in all helices in all proteins.     

Identification of a new gene mutated in Fraser syndrome and mouse myelencephalic blebs

Fraser syndrome is a recessive, multisystem disorder presenting with cryptophthalmos, syndactyly and renal defects and associated with loss-of-function mutations of the extracellular matrix protein FRAS1. Fras1 mutant mice have a blebbed phenotype characterized by intrauterine epithelial fragility generating serous and, later, hemorrhagic blisters. The myelencephalic blebs (my) strain has a similar phenotype. We mapped my to Frem2, a gene related to Fras1 and Frem1, and showed that a Frem2 gene-trap mutation was allelic to my. Expression of Frem2 in adult kidneys correlated with cyst formation in my homozygotes, indicating that the gene is required for maintaining the differentiated state of renal epithelia. Two individuals with Fraser syndrome were homozygous with respect to the same missense mutation of FREM2, confirming genetic heterogeneity. This is the only missense mutation reported in any blebbing mutant or individual with Fraser syndrome, suggesting that calcium binding in the CALXbeta-cadherin motif is important for normal functioning of FREM2.     

Tumour biology: senescence in premalignant tumours

Oncogene-induced senescence is a cellular response that may be crucial for protection against cancer development, but its investigation has so far been restricted to cultured cells that have been manipulated to overexpress an oncogene. Here we analyse tumours initiated by an endogenous oncogene, ras, and show that senescent cells exist in premalignant tumours but not in malignant ones. Senescence is therefore a defining feature of premalignant tumours that could prove valuable in the diagnosis and prognosis of cancer.