A solution to limited genomic capacity: using adaptable binding surfaces to assemble the functional HIV Rev oligomer on RNA

Many ribonucleoprotein (RNP) complexes assemble into large, organized structures in which protein subunits are positioned by interactions with RNA and other proteins. Here we demonstrate that HIV Rev, constrained in size by a limited viral genome, also forms an organized RNP by assembling a homo-oligomer on the Rev response element (RRE) RNA. Rev subunits bind cooperatively to discrete RNA sites using an oligomerization domain and an adaptable protein-RNA interface, forming a complex with 500-fold higher affinity than the tightest single interaction. High-affinity binding correlates strongly with RNA export activity. Rev utilizes different surfaces of its alpha-helical RNA-binding domain to recognize several low-affinity binding sites, including the well-characterized stem IIB site and an additional site in stem IA. We propose that adaptable RNA-binding surfaces allow the Rev oligomer to assemble economically into a discrete, stable RNP and provide a mechanistic role for Rev oligomerization during the HIV life cycle.     

Reproductive biology of Hechtia schottii, a dioecious Bromeliaceae, in Mexico

Hechtia schottii is a terrestrial, rosetofilous, dioecious, polycarpic succulent herb, that grows mainly in shrubby associations, and less frequently, in secondary low caducifolious forests, both on calcareous soils or limestone outcrops in Yucatan and Campeche States, Mexico. We studied phenology, floral and pollination biology, and breeding system at Calcehtok, Yucatan, during two flowering seasons. Plants bloom mainly during the dry season (November-April) and disperse seeds during the rainy season (May-October). Both floral morphs have diurnal anthesis; pollen is removed ca. 1 h after anthesis starts and both floral morphs are visited by several insect species, especially bees, but results suggest that the introduced honey bee, Apis mellifera, is the pollinator. Controlled crossings show that the species is functionally dioecious and requires to be serviced by pollinators based on fruit setting only in unassisted cross pollination crosses.     

Thermodynamics and dynamics of the formation of spherical lipid vesicles

We propose a free energy expression accounting for the formation of spherical vesicles from planar lipid membranes and derive a Fokker–Planck equation for the probability distribution describing the dynamics of vesicle formation. We find that formation may occur as an activated process for small membranes and as a transport process for sufficiently large membranes. We give explicit expressions for the transition rates and the characteristic time of vesicle formation in terms of the relevant physical parameters.     

Genome-Wide Screen of Genes Required for Caffeine Tolerance in Fission Yeast

Background

An excess of caffeine is cytotoxic to all eukaryotic cell types. We aim to study how cells become tolerant to a toxic dose of this drug, and the relationship between caffeine and oxidative stress pathways.

Methodology/Principal Findings

We searched for Schizosaccharomyces pombe mutants with inhibited growth on caffeine-containing plates. We screened a collection of 2,700 haploid mutant cells, of which 98 were sensitive to caffeine. The genes mutated in these sensitive clones were involved in a number of cellular roles including the H₂O₂-induced Pap1 and Sty1 stress pathways, the integrity and calcineurin pathways, cell morphology and chromatin remodeling. We have investigated the role of the oxidative stress pathways in sensing and promoting survival to caffeine. The Pap1 and the Sty1 pathways are both required for normal tolerance to caffeine, but only the Sty1 pathway is activated by the drug. Cells lacking Pap1 are sensitive to caffeine due to the decreased expression of the efflux pump Hba2. Indeed, ?hba2 cells are sensitive to caffeine, and constitutive activation of the Pap1 pathway enhances resistance to caffeine in an Hba2-dependent manner.

Conclusions/Significance

With our caffeine-sensitive, genome-wide screen of an S. pombe deletion collection, we have demonstrated the importance of some oxidative stress pathway components on wild-type tolerance to the drug.     

The INTERPRET Decision-Support System version 3.0 for evaluation of Magnetic Resonance Spectroscopy data from human brain tumours and other abnormal brain masses

Background  

Proton Magnetic Resonance (MR) Spectroscopy (MRS) is a widely available technique for those clinical centres equipped with MR scanners. Unlike the rest of MR-based techniques, MRS yields not images but spectra of metabolites in the tissues. In pathological situations, the MRS profile changes and this has been particularly described for brain tumours. However, radiologists are frequently not familiar to the interpretation of MRS data and for this reason, the usefulness of decision-support systems (DSS) in MRS data analysis has been explored.     

SpectraClassifier 1.0: a user friendly,automated MRS-based classifier-development system

Background  

SpectraClassifier (SC) is a Java solution for designing and implementing Magnetic Resonance Spectroscopy (MRS)-based classifiers. The main goal of SC is to allow users with minimum background knowledge of multivariate statistics to perform a fully automated pattern recognition analysis. SC incorporates feature selection (greedy stepwise approach, either forward or backward), and feature extraction (PCA). Fisher Linear Discriminant Analysis is the method of choice for classification. Classifier evaluation is performed through various methods: display of the confusion matrix of the training and testing datasets; K-fold cross-validation, leave-one-out and bootstrapping as well as Receiver Operating Characteristic (ROC) curves.     

Solid character of membrane ceramides: a surface rheology study of their mixtures with sphingomyelin

The compression and shear viscoelasticities of egg-ceramide and its mixtures with sphingomyelin were investigated using oscillatory surface rheology performed on Langmuir monolayers. We found high values for the compression and shear moduli for ceramide, compatible with a solid-state membrane, and extremely high surface viscosities when compared to typical fluid lipids. A fluidlike rheological behavior was found for sphingomyelin. Lateral mobilities, measured from particle tracking experiments, were correlated with the monolayer viscosities through the usual hydrodynamic relationships. In conclusion, ceramide increases the solid character of sphingomyelin-based membranes and decreases their fluidity, thus drastically decreasing the lateral mobilities of embedded objects. This mechanical behavior may involve important physiological consequences in biological membranes containing ceramides.     

Biomass recovery through secondary succession in the Cordillera Central de los Andes, Colombia

Estimations on biomass recovery rates by secondary tropical forests are needed to understand the complex tropical succession, and their importance on CO2 capture, to offset the warming of the planet. We conducted the study in the Porce River Canyon between 550 and 1 700m.a.s.l. covering tropical and premontane moist belts. We established 33 temporary plots of 50m x 20m in secondary forests, including fallows to succesional forests, and ranging between 3 and 36 years old; we measured the diameter at breast height (D) of all woody plants with D > or = 5cm. In each one of these plots we established five 10m x 10m subplots, in which we measured the diameter betweem 1cm < or = D < 5cm of all woody plants. We estimated the biomass of pastures by harvesting 54 plots of 2m x 2m, and of shrubs in the fallows by harvesting the biomass in 18 plots of 5m x 2m. We modeled Bav (above ground live biomass of woody plants) and Brg (coarse root biomass) as a function of succesional age (t) with the growth model of von Bertalanffy, using 247t/ha and 66t/ha as asymptote, respectively. Besides, we modeled the ratios brg/bav = f(D) and Brg/Bav = f(t). The model estimated that 87 years are required to recover the existing Bav of primary forests through secondary succession, and 217 years for the Brg of the primary forest. The maximum instantaneous growth rate of the Bav was 6.95 t/ha/yr at age 10. The maximum average growth rate of the Bav was 6.26 t/ha/yr at age 17. The weighted average of the absolute growth rate of the Bav reached 4.57t/ha/yr and the relative growth rate 10% annually. The ratio brg/bav decreases with increasing D. The ratio Brg/Bav initially increases very rapidly until age 5 (25%), then decreases to reach 25 years (18%) and increases afterwards until the ratio reaches the asymptote (26.7%).     

Synthesis and evaluation of 5-HT(2A) and 5-HT(2C) receptor binding affinities of novel pyrimidine derivatives

In an effort to find potential anxiolytic and/or antipsychotic agents with selective 5-HT(2C) affinity a series of new pyrimidine derivatives was prepared and the binding affinities for 5-HT(2A) and 5-HT(2C) receptors were determined.