PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships

Background  

Phylogenies, i.e., the evolutionary histories of groups of taxa, play a major role in representing the interrelationships among biological entities. Many software tools for reconstructing and evaluating such phylogenies have been proposed, almost all of which assume the underlying evolutionary history to be a tree. While trees give a satisfactory first-order approximation for many families of organisms, other families exhibit evolutionary mechanisms that cannot be represented by trees. Processes such as horizontal gene transfer (HGT), hybrid speciation, and interspecific recombination, collectively referred to as reticulate evolutionary events, result in networks, rather than trees, of relationships. Various software tools have been recently developed to analyze reticulate evolutionary relationships, which include SplitsTree4, LatTrans, EEEP, HorizStory, and T-REX.     

Photophysical properties of non-homoconjugated 1,2-dihydro, 1,2,3,4-tetrahydro and 1,2,3,4,5,6-hexahydro-C60 derivatives.

The photophysical properties of a novel series of non-homoconjugated 1,2-di-, 1,2,3,4-tetra-, and 1,2,3,4,5,6-hexasubstituted fullerenes (compounds 1, 2, and 3, respectively) have been systematically investigated. In this report, we examine the effect of substitution pattern of non-homoconjugated derivatized fullerenes on the ground state UV-Vis absorption, triplet state properties (lifetime, quantum yield, extinction coefficient), and singlet oxygen quantum yield. The non-homoconjugated fullerene derivatives 1-3 exhibit higher singlet oxygen quantum yield than analogous homoconjugated Bingel adducts with the same number of saturated C[double bond, length as m-dash]C bonds and exhibit decreasing quantum yield of singlet oxygen generation upon increasing the degree of functionalization on a single six member ring on the fullerene cage. This trend is similar for triplet quantum yield and triplet lifetime. The triplet extinction coefficient increases with functionalization. A detailed discussion comparing 1, 2, and 3 with functionalized homoconjugated systems and with other non-homoconjugated derivatives is presented.     

Adaptive evolution has targeted the C-terminal domain of the RXLR effectors of plant pathogenic oomycetes

Plant pathogenic microbes deliver effector proteins inside host cells to modulate plant defense circuitry and enable parasitic colonization. As genome sequences from plant pathogens become available, genome-wide evolutionary analyses will shed light on how pathogen effector genes evolved and adapted to the cellular environment of their host plants. In the August 2007 issue of Plant Cell, we described adaptive evolution (positive selection) in the cytoplasmic RXLR effectors of three recently sequenced oomycete plant pathogens. Here, we summarize our findings and describe additional data that further validate our approach.Key words: plant-microbe interactions, effectors, gene families, positive selectionA diverse number of plant pathogens, including bacteria, oomycetes, fungi and nematodes, deliver effector proteins inside host cells to modulate plant defense circuitry and enable parasitic colonization.^1–8 Because these so-called cytoplasmic effectors function inside plant cells and produce phenotypes that extend to plant cells and tissues, their genes are expected to be the direct target of the evolutionary forces that drive the antagonistic interplay between pathogen and host.^9,10 In a study published in the August 2007 issue of Plant Cell, we and our collaborators examined the extent to which positive selection (adaptive evolution) has shaped the evolution of the cytoplasmic effectors of three recently sequenced oomycete plant pathogens Phytophthora sojae, Phytophthora ramorum, and Hyaloperonospora parasitica (Genome Sequencing Center at Washington University).¹¹     

Anaerobic Nitrogen-Fixing Consortia Consisting of Clostridia Isolated from Gramineous Plants

We report here the existence of anaerobic nitrogen-fixing consortia (ANFICOs) consisting of N₂-fixing clostridia and diverse nondiazotrophic bacteria in nonleguminous plants; we found these ANFICOs while attempting to overcome a problem with culturing nitrogen-fixing microbes from various gramineous plants. A major feature of ANFICOs is that N₂ fixation by the anaerobic clostridia is supported by the elimination of oxygen by the accompanying bacteria in the culture. In a few ANFICOs, nondiazotrophic bacteria specifically induced nitrogen fixation of the clostridia in culture. ANFICOs are widespread in wild rice species and pioneer plants, which are able to grow in unfavorable locations. These results indicate that clostridia are naturally occurring endophytes in gramineous plants and that clostridial N₂ fixation arises in association with nondiazotrophic endophytes.     

Shrimp chitin as substrate for fungal chitin deacetylase

The fungal chitin deacetylases (CDA) studied so far are able to perform heterogeneous enzymatic deacetylation on their solid substrate, but only to a limited extent. Kinetic data show that about 5-10% of the N-acetyl glucosamine residues are deacetylated rapidly. Thereafter enzymatic deacetylation is slow. In this study, chitin was exposed to various physical and chemical conditions such as heating, sonicating, grinding, derivatization and interaction with saccharides and presented as a substrate to the CDA of the fungus Absidia coerulea. None of these treatments of the substrate resulted in a more efficient enzymatic deacetylation. Dissolution of chitin in specific solvents followed by fast precipitation by changing the composition of the solvent was not successful either in making microparticles that would be more accessible to the enzyme. However, by treating chitin in this way, a decrystallized chitin with a very small particle size called superfine (SF) chitin could be obtained. This SF chitin, pretreated with 18% formic acid, appeared to be a good substrate for fungal deacetylase. This was confirmed both by enzyme-dependent deacetylation measured by acetate production as well as by isolation and assay for the degree of deacetylation (DD). In this way chitin (10% DD) was deacetylated by the enzyme into chitosan with DD of 90%. The formic acid treatment reduced the molecular weight of the polymeric chain from 2x10(5) in chitin to 1.2 x 10(4) in the chitosan product. It is concluded that nearly complete enzymatic deacetylation has been demonstrated for low-molecular chitin.     

Effect of carbon sources on the induction of xylanolytic-cellulolytic multienzyme complexes in Paenibacillus curdlanolyticus strain B-6

The effect of polymeric substances such as alpha-cellulose, birchwood xylan, corn hull, and sugarcane bagasse, and of soluble sugars such as L-arabinose, D-galactose, D-glucose, D-xylose, and cellobiose, on the induction of multienzyme complexes in a facultatively anaerobic bacterium, Paenibacillus curdlanolyticus B-6, was investigated under aerobic conditions. Cells and culture supernatants of strain B-6 grown on different carbon sources were analyzed. Cells grown on each carbon source adhered to cellulose. Hence strain B-6 cells from all carbon sources must have an essential component responsible for anchoring the cells to the substrate surfaces. Native-polyacrylamide gel electrophoresis (native-PAGE), sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE), zymogram analysis, and enzymatic assays indicated that many proteins having xylanolytic and cellulolytic activities from P. curdlanolyticus B-6 grown on each carbon source were produced as two multienzyme complexes in the culture supernatants. These results indicate that P. curdlanolyticus B-6 produced multienzyme complexes when grown on both polymeric and soluble sugars. The multienzyme complexes of P. curdlanolyticus B-6 consisted of the main enzymes and non-enzymatic subunits and the production of some different subunits, depending on the carbon source.     

Novel anticancer agents, kayeassamins C-I from the flower of Kayea assamica of Myanmar

A CHCl3-soluble fraction of 70% EtOH extract of the flower of Kayea assamica from Myanmar exhibited 100% preferential cytotoxicity (PC(100)) against human pancreatic cancer PANC-1 cells under nutrient-deprived conditions at 1 microg/mL. Bioassay-guided fractionation and isolation afforded nine new coumarins, kayeassamins A (8), B (9), and C-I (1-7), together with nine known coumarins (10-18). The structures of these compounds were identified by extensive spectroscopic techniques as well as by comparison with published data. Absolute configuration at C-1' of 1 was established as S-configuration by the modified Mosher method. All the isolates were evaluated for their in vitro preferential cytotoxicity using novel anti-austerity strategy. Among them, the novel coumarins, kayeassamins A (8), B (9), D (2), E (3), and G (5) exhibited the most potent preferential cytotoxicity (PC(100) 1 microM) in a concentration- and time-dependent manner and induced apoptosis-like morphological changes of PANC-1 cells within 24 h of treatment. Based on the observed cytotoxicity, structure-activity relationships have been established.     

Vasoconstrictive effect of hydrogen sulfide involves downregulation of cAMP in vascular smooth muscle cells

Hydrogen sulfide (H(2)S), a new endogenous mediator, produces both vasorelaxation and vasoconstriction. This study was designed to examine whether cAMP mediates the vasoconstrictive effect of H(2)S. We found that NaHS at a concentration range of 10-100 microM (yields approximately 3-30 microM H(2)S) concentration-dependently reversed the vasodilation caused by isoprenaline and salbutamol, two beta-adrenoceptor agonists, and forskolin, a selective adenylyl cyclase activator, in phenylephrine-precontracted rat aortic rings. Pretreatment with NaHS (10-100 microM) for 5 min also significantly attenuated the vasorelaxant effect of salbutamol and forskolin. More importantly, NaHS (5-100 microM) significantly reversed forskolin-induced cAMP accumulation in vascular smooth muscle cells. However, NaHS produced significant, but weaker, vasoconstriction in the presence of N(G)-nitro-l-arginine methyl ester (100 microM), a nitric oxide synthase inhibitor, or in endothelium-denuded aortic rings. Blockade of ATP-sensitive potassium channels with glibenclamide (10 microM) failed to attenuate the vasoconstriction induced by H(2)S. Taken together, we demonstrated for the first time that the vasoconstrictive effect of H(2)S involves the adenyly cyclase/cAMP pathway.     

The cardiovascular effects of amodiaquine and structurally related antimalarials: An individual patient data meta-analysis

BackgroundAmodiaquine is a 4-aminoquinoline antimalarial similar to chloroquine that is used extensively for the treatment and prevention of malaria. Data on the cardiovascular effects of amodiaquine are scarce, although transient effects on cardiac electrophysiology (electrocardiographic QT interval prolongation and sinus bradycardia) have been observed. We conducted an individual patient data meta-analysis to characterise the cardiovascular effects of amodiaquine and thereby support development of risk minimisation measures to improve the safety of this important antimalarial.Methods and findingsStudies of amodiaquine for the treatment or prevention of malaria were identified from a systematic review. Heart rates and QT intervals with study-specific heart rate correction (QTcS) were compared within studies and individual patient data pooled for multivariable linear mixed effects regression.The meta-analysis included 2,681 patients from 4 randomised controlled trials evaluating artemisinin-based combination therapies (ACTs) containing amodiaquine (n = 725), lumefantrine (n = 499), piperaquine (n = 716), and pyronaridine (n = 566), as well as monotherapy with chloroquine (n = 175) for uncomplicated malaria. Amodiaquine prolonged QTcS (mean = 16.9 ms, 95% CI: 15.0 to 18.8) less than chloroquine (21.9 ms, 18.3 to 25.6, p = 0.0069) and piperaquine (19.2 ms, 15.8 to 20.5, p = 0.0495), but more than lumefantrine (5.6 ms, 2.9 to 8.2, p < 0.001) and pyronaridine (−1.2 ms, −3.6 to +1.3, p < 0.001). In individuals aged ≥12 years, amodiaquine reduced heart rate (mean reduction = 15.2 beats per minute [bpm], 95% CI: 13.4 to 17.0) more than piperaquine (10.5 bpm, 7.7 to 13.3, p = 0.0013), lumefantrine (9.3 bpm, 6.4 to 12.2, p < 0.001), pyronaridine (6.6 bpm, 4.0 to 9.3, p < 0.001), and chloroquine (5.9 bpm, 3.2 to 8.5, p < 0.001) and was associated with a higher risk of potentially symptomatic sinus bradycardia (≤50 bpm) than lumefantrine (risk difference: 14.8%, 95% CI: 5.4 to 24.3, p = 0.0021) and chloroquine (risk difference: 8.0%, 95% CI: 4.0 to 12.0, p < 0.001). The effect of amodiaquine on the heart rate of children aged <12 years compared with other antimalarials was not clinically significant. Study limitations include the unavailability of individual patient-level adverse event data for most included participants, but no serious complications were documented.ConclusionsWhile caution is advised in the use of amodiaquine in patients aged ≥12 years with concomitant use of heart rate–reducing medications, serious cardiac conduction disorders, or risk factors for torsade de pointes, there have been no serious cardiovascular events reported after amodiaquine in widespread use over 7 decades. Amodiaquine and structurally related antimalarials in the World Health Organization (WHO)-recommended dose regimens alone or in ACTs are safe for the treatment and prevention of malaria.

In this meta-analysis, Xin Hui Supanee Chan and colleagues investigate the cardiovascular effects of amodiaquine and structurally-related antimalarials using individual patient data from trials.