Does Variation in Genome Sizes Reflect Adaptive or Neutral Processes? New Clues from Passiflora

One of the long-standing paradoxes in genomic evolution is the observation that much of the genome is composed of repetitive DNA which has been typically regarded as superfluous to the function of the genome in generating phenotypes. In this work, we used comparative phylogenetic approaches to investigate if the variations in genome sizes (GS) should be considered as adaptive or neutral processes by the comparison between GS and flower diameters (FD) of 50 Passiflora species, more specifically, within its two most species-rich subgenera, Passiflora and Decaloba. For this, we have constructed a phylogenetic tree of these species, estimated GS and FD of them, inferred the tempo and mode of evolution of these traits and their correlations, using both current and phylogenetically independent contrasted values. We found significant correlations among the traits, when considering the complete set of data or only the subgenus Passiflora, whereas no correlations were observed within Decaloba. Herein, we present convincing evidence of adaptive evolution of GS, as well as clues that this pattern is limited by a minimum genome size, which could reduce both the possibilities of changes in GS and the possibility of phenotypic responses to environment changes.     

Optimisation of PD-FcY veterinary antigen secretion from Nicotiana benthamiana hairy roots and purification from the culture medium

Plant Cell, Tissue and Organ Culture (PCTOC) - Hairy roots (HR) are a promising plant tissue-based platform for the production of biopharmaceuticals as the secretion of recombinant proteins in the...     

Role(s) of formyl-peptide receptors expressed in nasal epithelial cells

Chronic rhinosinusitis is one of the most frequent chronic diseases in humans. Little is known about stimuli initiating tissue remodeling process that determines the morphological expression of the disease. N-formyl peptide receptors (FPRs) are innate immunity receptors important in tissue remodeling of gastric and intestinal epithelium. The expression and functions of FPRs in nasal epithelial cells were examined to evaluate whether they could be important in the remodeling of nasal mucosa. The aim of this study is to examine FPR expression in a nasal epithelial cell line (RPMI-2650) at mRNA and protein levels. To determine whether FPRs were functional, chemotaxis experiments were carried out. In addition the effects of FPRs agonists on the expression (PCR and ELISA) of VEGF-A and TGF-beta, two key mediators of tissue remodelling, were examined. Here we demonstrate that RPMI-2650 express FPR and FPRL2, but not FPRL1. fMLP, a bacterial product active on FPR, and uPAR(84-95), an inflammatory mediator agonist for FPRL2, stimulated migration of nasal epithelial cells. fMLP and uPAR(84-95) induce expression and secretion of VEGF-A and TGF-beta. Our results suggest a possible mechanisms initiating tissue remodeling observed during chronic rhinosinusitis. This study provides further evidence that FPRs play a more complex role in human pathophysiology than bacterial recognition.     

Cystic fibrosis gene variability in two southern Brazilian Amerindian populations: analysis of the deltaF508 mutation and the KM19 and XV2C haplotypes

The frequencies of the deltaF508 deletion, the most common cystic fibrosis mutation in Europeans and European-derived populations, and the XV2C and KM19 restriction fragment length polymorphisms that are tightly linked to the CFTR locus vary among populations. To determine the distribution of these extragenic markers and of the deltaF508 mutation, we analyzed 326 chromosomes of individuals from two South American Indian populations, the Guarani and the Kaingang. The allele and haplotype frequencies differed greatly between the two populations as well as among Amerindians and normal European Brazilians and European Brazilian cystic fibrosis patients. The absence of the deltaF508 mutation and the B haplotype are in agreement with the hypothesis that the deltaF508 mutation occurred after the divergence of these two populations. This finding is useful for populations containing a large Amerindian component and helps us to understand the origins of the deltaF508 deletion, the most common cystic fibrosis mutation in Europeans and European-derived populations, as well as the different incidences of cystic fibrosis in continental groups.     

Niger-Congo speaking populations and the formation of the Brazilian gene pool: mtDNA and Y-chromosome data

We analyzed sequence variation in the mitochondrial DNA (mtDNA) hypervariable segment I (HVS-I) from 201 Black individuals from two Brazilian cities (Rio de Janeiro and Porto Alegre), and compared these data with published information from 21 African populations. A subset of 187 males of the sample was also characterized for 30 Y-chromosome biallelic polymorphisms, and the data were compared with those from 48 African populations. The mtDNA data indicated that respectively 69% and 82% of the matrilineages found in Rio de Janeiro and Porto Alegre originated from West-Central/Southeast Africa. These estimates are in close agreement with historical records which indicated that most of the Brazilian slaves who arrived in Rio de Janeiro were from West-Central Africa. In contrast to mtDNA, Y-chromosome haplogroup analysis did not allow discrimination between places of origin in West or West-Central Africa. Thus, when comparing these two major African regions, there seems to be higher genetic structure with mtDNA than with Y-chromosome data.     

Prediction and course of symptoms and lung function around an exacerbation in chronic obstructive pulmonary disease

Background

Frequent exacerbations induce a high burden to Chronic Obstructive Pulmonary Disease (COPD). We investigated the course of exacerbations in the published COSMIC study that investigated the effects of 1-year withdrawal of fluticasone after a 3-month run-in treatment period with salmeterol/fluticasone in patients with COPD.

Methods

In 373 patients, we evaluated diary cards for symptoms, Peak Expiratory Flow (PEF), and salbutamol use and assessed their course during exacerbations.

Results

There were 492 exacerbations in 224 patients. The level of symptoms of cough, sputum, dyspnea and nocturnal awakening steadily increased from 2 weeks prior to exacerbation, with a sharp rise during the last week. Symptoms of cough, sputum, and dyspnea reverted to baseline values at different rates (after 4, 4, and 7 weeks respectively), whereas symptoms of nocturnal awakening were still increased after eight weeks. The course of symptoms was similar around a first and second exacerbation. Increases in symptoms and salbutamol use and decreases in PEF were associated with a higher risk to develop an exacerbation, but with moderate predictive values, the areas under the receiver operating curves ranging from 0.63 to 0.70.

Conclusions

Exacerbations of COPD are associated with increased symptoms that persist for weeks and the course is very similar between a first and second exacerbation. COPD exacerbations are preceded by increased symptoms and salbutamol use and lower PEF, yet predictive values are too low to warrant daily use in clinical practice.     

Use of unsupervised and supervised artificial neural networks for the identification of lactic acid bacteria on the basis of SDS-PAGE patterns of whole cell proteins

Conventional multivariate statistical techniques (hierarchical cluster analysis, linear discriminant analysis) and unsupervised (Kohonen Self Organizing Map) and supervised (Bayesian network) artificial neural networks were compared for as tools for the classification and identification of 352 SDS-PAGE patterns of whole cell proteins of lactic acid bacteria belonging to 22 species of the genera Lactobacillus, Leuconostoc, Enterococcus, Lactococcus and Streptococcus including 47 reference strains. Electrophoretic data were pre-treated using the logistic weighting function described by Piraino et al. [Piraino, P., Ricciardi, A., Lanorte, M. T., Malkhazova, I., Parente, E., 2002. A new procedure for data reduction in electrophoretic fingerprints of whole-cell proteins. Biotechnol. Lett. 24, 1477-1482]. Hierarchical cluster analysis provided a satisfactory classification of the patterns but was unable to discriminate some species (Leuconostoc, Lb. sakei/Lb. curvatus, Lb. acidophilus/Lb. helveticus, Lb. plantarum/Lb. paraplantarum, Lc. lactis/Lc. raffinolactis). A 7x7 Kohonen self-organizing map (KSOM), trained with the patterns of the reference strains, provided a satisfactory classification of the patterns and was able to discriminate more species than hierarchical cluster analysis. The map was used in predictive mode to identify unknown strains and provided results which in 85.5% of cases matched the classification obtained by hierarchical cluster analysis. Two supervised tools, linear discriminant analysis and a 23:5:2 Bayesian network were proven to be highly effective in the discrimination of SDS-PAGE patterns of Lc. lactis from those of other species. We conclude that data reduction by logistic weighting coupled to traditional multivariate statistical analysis or artificial neural networks provide an effective tool for the classification and identification of lactic acid bacteria on the basis of SDS-PAGE patterns of whole cell proteins.     

Bioactive lipopeptides of ice-nucleating snow bacterium Pseudomonas syringae strain 31R1

The production of secondary metabolite lipopeptides by ice-nucleating Pseudomonas syringae strain 31R1 was investigated. Pseudomonas syringae strain 31R1 is a rifampicin-resistant derivative of P. syringae no. 31 used for the commercial production of snow. It is shown that P. syringae strain 31R1 produces antifungal lipodepsipeptides, syringomycins E and G, and, in addition, a novel and unique lipopeptide, peptin31. Spectroscopic and spectrometric analyses revealed that peptin31 is a linear undecalipopeptide with sequence identities to N- and C-terminal portions but lacking 11 amino acids of known lipodepsipeptide syringopeptin SPPhv. Peptin31 displayed antifungal activities against Rhodotorula pilimanae, Rhizoctonia solani, and Trichoderma harzianum and also hemolytic and antibacterial activities. Extracts of P. syringae strain 31R1 grown in medium with chloride were fungicidal, but not when grown without chloride. The latter extracts lacked peptin 31 and contained des-chloro forms of syringomycins E and G with low antifungal activities. Thus, the three lipopeptides account for the fungicidal properties of P. syringae 31R1 extracts. The occurrence of these bioactive metabolites should be considered when P. syringae no. 31 and its derivatives are used in products for making artificial snow.     

Isolation and characterization of Oenococcus oeni from Aglianico wines

A technological characterization of Oenococcus oeni strains isolated from Aglianico wines was performed to select starter cultures for malolactic fermentation (MLF). One hundred and fifty six O. oeni isolates were extracted from Aglianico wines, and identified by using species-specific PCR. Malolactic activity (MLA), sulphur dioxide (SO₂) resistance, acetaldehyde metabolism and other technological characteristics were tested. Differences in the technologically relevant characteristics were observed. All O. oeni strains were able to grow at low temperature and none in presence of 14% of ethanol. About 80% of O. oeni degraded more than 80% of acetaldehyde, producing ethanol and acetic acid as final products. Among nine O. oeni chosen, four isolates were sensitive to 60 mg of SO₂ l⁻¹, while the other five had high resistance. Considering their technological characteristics, five O. oeni strains could be selected starter cultures for MLF in Aglianico.     

Genetic, geographic, and linguistic variation among South American Indians: possible sex influence.

To better understand the relationship between genetic variability, geographical distance, and linguistic affiliation in South Amerinds, and to elucidate whether the migration rate is the same for both sexes, spatial autocorrelation, Mantel's test, and F(ST) analyses were performed in four sets of populations and alleles (group 1: 48 populations, 12 alleles; group 2: 16 (all belonging to the Tupi linguistic group) and 12; group 3: 21 and 17; and group 4: 28 and 4 haplotypes). Groups 1-3 included blood group and protein (i.e., serum protein, red cell enzymes, and immunoglobulin systems), while group 4 was concerned with mitochondrial DNA (mtDNA) only. The latter set was also subjected to a molecular analysis of variance (AMOVA) evaluation. The frequencies of statistically significant correlograms were lower than those obtained in other populations when the blood groups and protein systems were considered, but 3 of the 4 mtDNA haplogroups gave suggestions of population structure. The variability in this organelle is also significantly correlated with language when geography is held constant. Migration per generation is generally low, but higher estimates were obtained for females. The AMOVA results suggest that populations whose members speak the same language are genetically homogeneous and may be viewed as the ultimate evolutionary unit at this level of analysis.