TreeSAAP: selection on amino acid properties using phylogenetic trees

The software program TreeSAAP measures the selective influences on 31 structural and biochemical amino acid properties during cladogenesis, and performs goodness-of-fit and categorical statistical tests.     

Direct haplotyping of kilobase-size DNA using carbon nanotube probes

We have implemented a method for multiplexed detection of polymorphic sites and direct determination of haplotypes in 10-kilobase-size DNA fragments using single-walled carbon nanotube (SWNT) atomic force microscopy (AFM) probes. Labeled oligonucleotides are hybridized specifically to complementary target sequences in template DNA, and the positions of the tagged sequences are detected by direct SWNT tip imaging. We demonstrated this concept by detecting streptavidin and IRD800 labels at two different sequences in M13mp18. Our approach also permits haplotype determination from simple visual inspection of AFM images of individual DNA molecules, which we have done on UGT1A7, a gene under study as a cancer risk factor. The haplotypes of individuals heterozygous at two critical loci, which together influence cancer risk, can be easily and directly distinguished from AFM images. The application of this technique to haplotyping in population-based genetic disease studies and other genomic screening problems is discussed.     

A novel motility pattern in quail spermatozoa with implications for the mechanism of flagellar beating

Background information. The spermatozoon of the quail (Coturnix coturnix L., var japonica) has a ‘9+2’ flagellum that is unusually long. When it moves in a viscous medium, near to the coverslip, it develops a meander waveform. Because of the high viscosity, the meander bends are static in relation to the field of view; bend propagation is therefore manifest as the forward movement of the flagellum through the meander shape. At the same time, the origin of the oscillation typically shifts proximally in a stepwise fashion. These movements have been analysed in the hope of contributing to the resolution of problems in flagellar mechanics. Results. (1) Meander waves originate from spontaneous sigmoid bend complexes. (2) On a given flagellum, fully developed meander bends are uniform in their large angle, curvature and propagation speed; interbends can vary in length and shape. (3) No intra‐axonemal sliding is transmitted through formed bends; sliding related to new bends is accommodated proximally. (4) Sliding reversal is initiated at a threshold shear angle of approx. 1 rad. (5) The arc wavespeed is the product of the arc wavelength and the beat frequency. (6) Physical obstruction to bend development causes a pause in the oscillation. (7) New bend initiation can thus be dissociated from bend propagation on the distal flagellum. (8) The steps in the forward advance of the oscillation site occur during the early phase of bend growth. Conclusions. (1) The main conclusion is that, in meander waves, the mechanical basis of the oscillation appears to be that the propulsive thrust arising from bend propagation acts as a bending stress to trigger sliding reversal, thus perpetuating the rhythmic beating. (2) Oscillations can originate at any position, provided the position is distal to a location where doublet sliding is restrained. (3) Meander waves are an example of new bend development without ‘paradoxical’ classes of sliding.     

NADPH Oxidase-generated Hydrogen Peroxide Induces DNA Damage in Mutant FLT3-expressing Leukemia Cells

Internal tandem duplication of the FMS-like tyrosine kinase (FLT3-ITD) receptor is present in 20% of acute myeloid leukemia (AML) patients and it has been associated with an aggressive AML phenotype. FLT3-ITD expressing cell lines have been shown to generate increased levels of reactive oxygen species (ROS) and DNA double strand breaks (DSBs). However, the molecular basis of how FLT3-ITD-driven ROS leads to the aggressive form of AML is not clearly understood. Our group has previously reported that inhibition of FLT3-ITD signaling results in post-translational down-regulation of p22^phox, a small membrane-bound subunit of the NADPH oxidase (NOX) complex. Here we demonstrated that 32D cells, a myeloblast-like cell line transfected with FLT3-ITD, have a higher protein level of p22^phox and p22^phox-interacting NOX isoforms than 32D cells transfected with the wild type FLT3 receptor (FLT3-WT). The inhibition of NOX proteins, p22^phox, and NOX protein knockdowns caused a reduction in ROS, as measured with a hydrogen peroxide (H₂O₂)-specific dye, peroxy orange 1 (PO1), and nuclear H₂O₂, as measured with nuclear peroxy emerald 1 (NucPE1). These reductions in the level of H₂O₂ following the NOX knockdowns were accompanied by a decrease in the number of DNA DSBs. We showed that 32D cells that express FLT3-ITD have a higher level of both oxidized DNA and DNA DSBs than their wild type counterparts. We also observed that NOX4 and p22^phox localize to the nuclear membrane in MV4–11 cells expressing FLT3-ITD. Taken together these data indicate that NOX and p22^phox mediate the ROS production from FLT3-ITD that signal to the nucleus causing genomic instability.     

Water availability alters the tri-trophic consequences of a plant-fungal symbiosis

Plant–microbe protection symbioses occur when a symbiont defends its host against enemies (e.g., insect herbivores); these interactions can have important influences on arthropod abundance and composition. Understanding factors that generate context-dependency in protection symbioses will improve predictions on when and where symbionts are most likely to affect the ecology and evolution of host species and their associated communities. Of particular relevance are changes in abiotic contexts that are projected to accompany global warming. For example, increased drought stress can enhance the benefits of fungal symbiosis in plants, which may have multi-trophic consequences for plant-associated arthropods. Here, we tracked colonization of fungal endophyte-symbiotic and aposymbiotic Poa autumnalis (autumn bluegrass) by Rhopalosiphum padi (bird-cherry-oat aphids) and their parasitoids (Aphelinus sp.) following manipulations of soil water levels. Endophyte symbiosis significantly reduced plant colonization by aphids. Under low water, symbiotic plants also supported a significantly higher proportion of aphids that were parasitized by Aphelinus and had higher above-ground biomass than aposymbiotic plants, but these endophyte-mediated effects disappeared under high water. Thus, the multi-trophic consequences of plant-endophyte symbiosis were contingent on the abiotic context, suggesting the potential for complex responses in the arthropod community under future climate shifts.     

Newly discovered linkages between the cortical (pellicular) ridges of Opalina

Samples of Opalina ranarum have been prepared for electron microscopy by ultra-rapid cryofixation followed by substitution fixation in a solvent containing tannic acid. This technique has made it possible to see that very thin linkages exist between the pleated ridges that form the surface of the cell. Between any two adjacent cortical ridges, the linkages, which are approximately 0.1 μm long, occur as a single row, 0.1 μm below the free edge, with an impressively regular spacing of 0.1 μm. The cortical ridges of the Opalinids are spaced with remarkable uniformity, even when thrown into undulating patterns. The linkages described here will inevitably stabilize the complex architecture of the cortex. Other possible functions are discussed.     

H2O2 production downstream of FLT3 is mediated by p22phox in the endoplasmic reticulum and is required for STAT5 signalling

The internal tandem duplication (ITD) of the juxtamembrane region of the FLT3 receptor has been associated with increased reactive oxygen species (ROS) generation in acute myeloid leukemia (AML). How this elevated level of ROS contributes to the leukemic phenotype, however, remains poorly understood. In this work we show that ROS in the FLT3-ITD expressing AML cell line MV4-11 is reduced by treatment with PKC412, an inhibitor of FLT3, DPI, a flavoprotein inhibitor, and VAS2870, a Nox specific inhibitor, suggesting that ROS production is both FLT3 and NADPH oxidase dependent. The majority of these ROS co-localize to the endoplasmic reticulum (ER), as determined with the H(2)O(2)-specific aryl-boronate dye Peroxyorange 1, which also corresponds to co-localization of p22phox. Moreover, knocking down p22phox dramatically reduces H(2)O(2) after 24 hours in the ER, without affecting mitochondrial ROS. Significantly, the FLT3 inhibitor PKC412 reduces H(2)O(2) in FLT3-ITD expressing cell lines (MV4-11, MOLM-13) through reduction of p22phox over 24 hours. Reduced p22phox is achieved by proteasomal degradation and is prevented upon GSK3-β inhibition. Knockdown of p22phox resulted in reduced STAT5 signalling and reduced Pim-1 levels in the cells after 24 hours. Thus, we have shown that FLT3 driven H(2)O(2) production in AML cells is mediated by p22phox and is critical for STAT5 signalling.