The phylogenetic analysis of variable-length sequence data: elongation factor-1alpha introns in European populations of the parasitoid wasp genus Pauesia (Hymenoptera: Braconidae: Aphidiinae)

Elongation factor-1alpha (EF-1alpha) is a highly conserved nuclear coding gene that can be used to investigate recent divergences due to the presence of rapidly evolving introns. However, a universal feature of intron sequences is that even closely related species exhibit insertion and deletion events, which cause variation in the lengths of the sequences. Indels are frequently rich in evolutionary information, but most investigators ignore sites that fall within these variable regions, largely because the analytical tools and theory are not well developed. We examined this problem in the taxonomically problematic parasitoid wasp genus Pauesia (Hymenoptera: Braconidae: Aphidiinae) using congruence as a criterion for assessing a range of methods for aligning such variable-length EF-1alpha intron sequences. These methods included distance- and parsimony-based multiple-alignment programs (CLUSTAL W and MALIGN), direct optimization (POY), and two "by eye" alignment strategies. Furthermore, with one method (CLUSTAL W) we explored in detail the robustness of results to changes in the gap cost parameters. Phenetic-based alignments ("by eye" and CLUSTAL W) appeared, under our criterion, to perform as well as more readily defensible, but computationally more demanding, methods. In general, all of our alignment and tree-building strategies recovered the same basic topological structure, which means that an underlying phylogenetic signal remained regardless of the strategy chosen. However, several relationships between clades were sensitive both to alignment and to tree-building protocol. Further alignments, considering only sequences belonging to the same group, allowed us to infer a range of phylogenetic relationships that were highly robust to tree-building protocol. By comparing these topologies with those obtained by varying the CLUSTAL parameters, we generated the distribution area of congruence and taxonomic compatibility. Finally, we present the first robust estimate of the European Pauesia phylogeny by using two EF-1alpha introns and 38 taxa (plus 3 outgroups). This estimate conflicts markedly with the traditional subgeneric classification. We recommend that this classification be abandoned, and we propose a series of monophyletic species groups.     

Atomistic Study of Lipid Membranes Containing Chloroform: Looking for a Lipid-Mediated Mechanism of Anesthesia

The molecular mechanism of general anesthesia is still a controversial issue. Direct effect by linking of anesthetics to proteins and indirect action on the lipid membrane properties are the two hypotheses in conflict. Atomistic simulations of different lipid membranes subjected to the effect of small volatile organohalogen compounds are used to explore plausible lipid-mediated mechanisms. Simulations of homogeneous membranes reveal that electrostatic potential and lateral pressure transversal profiles are affected differently by chloroform (anesthetic) and carbon tetrachloride (non-anesthetic). Simulations of structured membranes that combine ordered and disordered regions show that chloroform molecules accumulate preferentially in highly disordered lipid domains, suggesting that the combination of both lateral and transversal partitioning of chloroform in the cell membrane could be responsible of its anesthetic action.     

Variability of the mc1r Gene in Melanic and Non-Melanic Podarcis lilfordi and Podarcis pityusensis from the Balearic Archipelago

The association between polymorphism at the mc1r locus and colour variation was studied in two wall lizard species (Podarcis lilfordi and P. pityusensis) from the Balearic archipelago. Podarcis lilfordi comprises several deep mitochondrial lineages, the oldest of which originated in the Pliocene, while much shallower mitochondrial lineages are found in P. pityusensis. Here, we examined whether specific substitutions were associated with the melanic colouration found in islet populations of these species. Homologous nuclear sequences covering most of the mc1r gene were obtained from 73 individuals from melanic and non-melanic Podarcis from different populations (the entire gene was also sequenced in six selected individuals). MtDNA gene trees were also constructed and used as a framework to assess mc1r diversity. Mc1r showed greater polymorphism in P. lilfordi than in P. pityusensis. However, we observed no substitutions that were common to all melanic individuals across the two species. Only one significant association was detected in the mc1r partial sequence, but this was a synonymous A/G mutation with A alleles being more abundant in melanic populations. In addition, there were no associations between the main dominant phenotypes (green and brown, blue and yellow spots and ventral colour) and synonymous or non-synonymous substitutions in the mc1r gene. There was no statistical evidence of selection on mc1r. This study suggests no relationship between mc1r polymorphism and colour variation in Balearic Podarcis.     

Fermentation of glycerol and production of valuable chemical and biofuel molecules

Glycerol has attracted the attention of scientific and industrial communities due to its generation in bulk quantities as a byproduct of biofuel industries. With the rapid growth of these industries in recent years, glycerol is frequently treated as a very low-value byproduct or even a waste product with a disposal cost associated to it. Glycerol is not only abundant and inexpensive but also can generate more reducing equivalents than glucose or xylose. This unique characteristic of glycerol offers a tremendous opportunity for its biological conversion to valuable products at higher yield. This review focuses on research efforts to utilize glycerol as a carbon source for the production of a variety of fuels and chemicals by both native and metabolically engineered microorganisms.     

Modeling pulsatile flow in aortic aneurysms: effect of non-Newtonian properties of blood

Pulsatile flow in an axisymmetric rigid-walled model of an abdominal aorta aneurysm was analyzed numerically for various aneurysm dilations using physiologically realistic resting waveform at time-averaged Reynolds number of 300 and peak Reynolds number of 1607. Discretization of the governing equations was achieved using a finite element scheme based on the Galerkin method of weighted residuals. Comparisons with previously published work on the basis of special cases were performed and found to be in excellent agreement. Our findings indicate that the velocity fields are significantly affected by non-Newtonian properties in pathologically altered configurations. Non-Newtonian fluid shear stress is found to be greater than Newtonian fluid shear stress during peak systole. Further, the maximum shear stress is found to occur near the distal end of AAA during peak systole. The impact of non-Newtonian blood flow characteristics on pressure compared to Newtonian model is found insignificant under resting conditions. Viscous and inertial forces associated with blood flow are responsible for the changes in the wall that result in thrombus deposition and dilation while rupture of AAA is more likely determined by much larger mechanical stresses imposed by pulsatile pressure on the wall of AAA.     

Field Evaluation of Steinernema feltiae Against the Web-spinning Larch Sawfly Cephalcia lariciphila

Field trials were conducted in Rheola Forest, Wales, Great Britain, to determine the effectiveness of Steinernema feltiae UK strain in controlling the web-spinning larch sawfly Cephalcia lariciphila. Foliar sprays at the rate of 5,000-20,000 nematodes/100 cm branch resulted in 3.4-29.4% infection of sawfly larvae. Soil application of 200 nematodes/cm² resulted in 61% infection of sawfly prepupae and 17.3% of pupae. Prepupal infection ranged from 4.8 to 14.7% 1 year after nematode application. Soil applications of this nematode show that it has potential for biological control of sawfly prepupae.     

Iron nutrition of a hydroponic strawberry culture (Fragaria vesca L.) supplied with different Fe chelates

Several indexes are used to determine the iron nutritional status of plants, but their effectiveness depends either on the plant growth conditions in natural environments or on the assay conditions. This research was conducted to test different indexes of the iron nutritional status of a hydroponic strawberry culture where treatments mainly differed in the source of the iron applied: Fe-EDTA, Fe-EDDHA and Fe-polyflavonoid. Macro and micronutrient concentrations in the nutrient solutions, leaf and vascular tissues were measured. Fe concentration in the nutrient solution during the course of the experiment was considered in relation to the stability of the different chelates. Both Fe concentration and total Fe content of leaves reflected the effect of the treatments; Fe/Mn ratio was significant as a diagnosis index. Other element ratios as P/Fe and K/Ca are not well related with the iron nutrition symptoms observed. Fe²⁺ concentration measured in leaves was not directly affected by the different chelate treatments.