Activation of Phenylalanine Hydroxylase Induces Positive Cooperativity toward the Natural Cofactor

Protein misfolding with loss-of-function of the enzyme phenylalanine hydroxylase (PAH) is the molecular basis of phenylketonuria in many individuals carrying missense mutations in the PAH gene. PAH is complexly regulated by its substrate l-Phenylalanine and its natural cofactor 6R-l-erythro-5,6,7,8-tetrahydrobiopterin (BH₄). Sapropterin dihydrochloride, the synthetic form of BH₄, was recently approved as the first pharmacological chaperone to correct the loss-of-function phenotype. However, current knowledge about enzyme function and regulation in the therapeutic setting is scarce. This illustrates the need for comprehensive analyses of steady state kinetics and allostery beyond single residual enzyme activity determinations to retrace the structural impact of missense mutations on the phenylalanine hydroxylating system. Current standard PAH activity assays are either indirect (NADH) or discontinuous due to substrate and product separation before detection. We developed an automated fluorescence-based continuous real-time PAH activity assay that proved to be faster and more efficient but as precise and accurate as standard methods. Wild-type PAH kinetic analyses using the new assay revealed cooperativity of activated PAH toward BH₄, a previously unknown finding. Analyses of structurally preactivated variants substantiated BH₄-dependent cooperativity of the activated enzyme that does not rely on the presence of l-Phenylalanine but is determined by activating conformational rearrangements. These findings may have implications for an individualized therapy, as they support the hypothesis that the patient''s metabolic state has a more significant effect on the interplay of the drug and the conformation and function of the target protein than currently appreciated.     

Evolutionary placement of Xanthomonadales based on conserved protein signature sequences

Xanthomonadales comprises one of the largest phytopathogenic bacterial groups, and is currently classified within the gamma-proteobacteria. However, the phylogenetic placement of this group is not clearly resolved, and the results of different studies contradict one another. In this work, the evolutionary position of Xanthomonadales was determined by analyzing the presence of shared insertions and deletions (INDELs) in highly conserved proteins. Several distinctive insertions found in most of the members of the gamma-proteobacteria are absent in Xanthomonadales and groups such as Legionelalles, Chromatiales, Methylococcales, Thiotrichales and Cardiobacteriales. These INDELs were most likely introduced after the branching of Xanthomonadales from most of the gamma-proteobacteria and provide evidence for the phylogenetic placement of the early gamma-proteobacteria. Moreover, other proteins contain insertions exclusive to the Xanthomonadales order, confirming that this is a monophyletic group and provide important specific genetic markers. Thus, the data presented clearly support the Xanthomonadales group as an independent subdivision, and constitute one of the deepest branching lineage within the gamma-proteobacteria clade.     

Tradicional use of medicinal plants with diuretic properties at Quemado de Güines Municipality, Cuba

Medicinal plants are highly rich in Cuba and an amount of 179 species have been reported to be used by the population for diuretic purposes, nevertheless, no experimental validation has supported this effect. This study presents the relative importance of the medicinal plant species most widely used for diuretic purposes in two communities of Quemado de Guines Municipality, Villa Clara province. The information was obtained through the application of an interview to 85 inhabitants, from which 80 were random surveys to people with a great knowledge of plants, and five to herbalists and doctors practicing natural medicine. The etnopharmacological information was registered (gathered) by means of the "Tradicional of the Medicine of the Island" (TRAMIL) methodology and the interesting species were identified by a botanist and deposited in the Herbarium of the Central University "Marta Abreu" from Villa Clara, registered in the Index Herbarium, published periodically by the International Association for Plant Taxonomy. The data was analyzed by means of the indexes of use values and significant use level after TRAMIL. From the total of 19 botanical families, 26 medicinal species were identified, and 10 plants resulted with higher significant use and higher indexes of use values. From the plants reported as diuretics, 53.8% have not been experimentally validated in Cuba, the rest of the identified species have been validated at a preclinical level in some centers in the country, but its use have not been authorized as phytochemicals by the Cuban Regulatory Agency. The documentation related to the use of medicinal plants in the studied areas reveals that the traditional knowledge continues deeply rooted in the communities, and popular wisdom is kept through the representative images of the herbalist and people with considerable knowledge about this topic.     

Targeted manipulation of leaf form via local growth repression

A classical view is that leaf shape is the result of local promotion of growth linked to cell proliferation. However, an alternative hypothesis is that leaf form is the result of local repression of growth in an otherwise growing system. Here we show that leaf form can indeed be manipulated in a directed fashion by local repression of growth. We show that targeting expression of an inhibitor of a cyclin-dependent kinase (KRP1) to the sinus area of developing leaves of Arabidopsis leads to local growth repression and the formation of organs with extreme lobing, including generation of leaflet-like organs. Directing KRP1 expression to other regions of the leaf using an miRNA target sequence tagging approach also leads to predictable novel leaf forms, and repression of growth in the leaf margin blocks the outgrowth of lobes, leading to a smoother perimeter. In addition, we show that decreased growth around the perimeter and across the leaf abaxial surface leads to a change in 3D form, as predicted by mechanical models of leaf growth. Our analysis provides experimental evidence that local repression of growth influences leaf shape, suggesting that it could be part of the mechanism of morphogenesis in plants in the context of an otherwise growing system.     

Repeatability of Quantitative MRI Measurements in Normal Breast Tissue

PURPOSE: To evaluate the variability and repeatability of repeated magnetic resonance imaging (MRI) measurements in normal breast tissues between and within subjects. METHODS: Eighteen normal premenopausal subjects underwent two contrast-enhanced MRI scans within 72 hours or during the same menstrual phase in two consecutive months. A subset of nine women also completed diffusion-weighted imaging (DWI). Fibroglandular tissue (FGT) density and FGT enhancement were measured on the contrast-enhanced MRI. Apparent diffusion coefficient (ADC) values were computed from DWI. Between- and within-subject coefficients of variation (bCV and wCV, respectively) were assessed. Repeatability of all measurements was assessed by the coefficient of repeatability (CR) and Bland-Altman plots. RESULTS: The bCV of FGT density and FGT enhancement at visit 1 and visit 2 ranged from 47% to 63%. The wCV was 13% for FGT density, 22% for FGT enhancement, and 11% for ADC. The CRs of FGT density and FGT enhancement were 0.15 and 0.19, respectively, and for ADC, it was 6.1 x 10^-4 mm²/s. CONCLUSIONS: We present an estimate of the variability and repeatability of MR measurements in normal breasts. These estimates provide the basis for understanding the normal variation of healthy breast tissue in MRI and establishing thresholds for agreement between measurements.     

Getting here from there: testing the genetic paradigm underpinning introduction histories and invasion success

Aim To explore the potential of genetic processes and mating systems to influence successful plant invasions, we compared genetic diversity of the highly invasive tropical treelet, Miconia calvescens, in nine invasive populations and three native range populations. Specifically, we tested how genetic diversity is partitioned in native and invaded regions, which have different invasion histories (multiple vs. single introductions). Lastly, we infer how levels of inbreeding in different regions impact invasion success. Location Invaded ranges in the Pacific (Hawaii, Tahiti, New Caledonia) and Australia and native range in Costa Rica. Methods Genetic diversity was inferred by analysing variation at nine microsatellite loci in 273 individuals from 13 populations of M. calvescens. Genetic structure was assessed using amova , isolation by distance (IBD) within regions, a Bayesian clustering approach, and principal coordinates analysis. Results Microsatellite analysis revealed that invaded regions exhibit low levels of allelic richness and genetic diversity with few private alleles. To the contrary, in the native range, we observed high levels of allelic richness, high heterozygosity and 78% of all private alleles. Surprisingly, despite evident genetic bottlenecks in all invasive regions, similarly high levels of inbreeding were detected in both invasive and native ranges (F_IS: 0.345 and 0.399, respectively). Bayesian clustering analysis showed a lack of geographical structure in the Pacific and evidence of differing invasion histories between the Pacific and Australia. While Pacific populations are derived from a single introduction to the region, multiple introductions have taken place in Australia from different source regions. Main conclusions Multiple introductions have not resulted in increased genetic diversity for M. calvescens invasions. Moreover, similar inbreeding levels between native and invaded ranges suggests that there is no correlation between levels of inbreeding and levels of standing genetic diversity for M. calvescens. Overall, our results show that neither inbreeding nor low genetic diversity is an impediment to invasion success.     

GOBASE--a database of mitochondrial and chloroplast information

GOBASE is a relational database containing integrated sequence, RNA secondary structure and biochemical and taxonomic information about organelles. GOBASE release 6 (summer 2002) contains over 130 000 mitochondrial sequences, an increase of 37% over the previous release, and more than 30 000 chloroplast sequences in a new auxiliary database. To handle this flood of new data, we have designed and implemented GOpop, a Java system for population and verification of the database. We have also implemented a more powerful and flexible user interface using the PHP programming language. http://megasun.bch.umontreal.ca/gobase/gobase.html.