Molecular phylogeny and biogeographic history of the piculets (Piciformes: Picumninae)

The subfamily Picumninae (piculets) includes 3 genera and 30 species of tiny and short-tailed woodpeckers with a pantropical distribution. Within the Picumninae, two cases of intercontinentally disrupted distributions at the genus level occur. The first one concerns the genus Sasia (one species in Africa and two in southeast Asia) while the second concerns Picumnus (one species in southeast Asia and 25 in South America). These disrupted distributions, as well as several morphological differences, have lead some authors to place the African representative of Sasia and the southeast Asian representative of Picumnus in their own monotypic genera ( Verreauxia and Vivia , respectively). To address the taxonomic status and biogeographic history of the piculets, we sequenced 2676 bp of DNA from one mitochondrial (ND2) and two nuclear markers (myoglobin intron 2 and β-fibrinogen intron 7). Monophyly of Picumninae could not be recovered with confidence, while monophyly of Sasia and Picumnus were always strongly supported. Molecular dating analyses revealed that the splits both between the African and Indo-Malayan Sasia and between the New World and Old World Picumnus occurred at ca 7.9 Myr BP. This time corresponds to the beginning of the formation of the northern Hemisphere ice sheets and the accompanying expansion of grasslands throughout the world. The spread of open areas in the northern parts of Eurasia and America prevented gene flow between tropical forest birds, such as the piculets, in Africa, southeast Asia and South America, respectively.     

Thermostable carbohydrate-binding modules in affinity chromatography

Affinity chromatography is routinely used mostly on a preparative scale to isolate different biomolecules such as proteins and carbohydrates. To this end a variety of proteins is in common use as ligands. To extend the arsenal of binders intended for separation of carbohydrates, we have explored the use of carbohydrate-binding modules (CBM) in affinity chromatography. The thermostable protein CBM4-2 and two variants (X-6 and A-6) thereof, selected from a newly constructed combinatorial library, were chosen for this study. The CBM4-2 predominantly binds to xylans but also crossreacts with glucose-based oligomers. The two CBM-variants X-6 and A-6 had been selected for binding to xylan and Avicel (a mixture of amorphous and microcrystalline cellulose), respectively. To assess the ability of these proteins to separate carbohydrates, they were immobilized to macroporous microparticulate silica and analyses were conducted at temperatures ranging from 25 to 65 degrees C. With the given set of CBM-variants, we were able to separate cello- and xylo-oligomers under isocratic conditions. The affinities of the CBMs for their targets were weak (in the mM-microM range) and by adjusting the column temperature we could optimize peak resolution and chromatographic retention times. The access to thermostable CBM-variants with diverse affinities and selectivities holds promise to be an efficient tool in the field of affinity chromatography for the separation of carbohydrates.     

Hybrids and fruit set in a mixed flowering-time population of Gymnadenia conopsea (Orchidaceae)

We have recently found that the morphologically determined subspecies Gymnadenia conopsea ssp conopsea in Sweden includes early and late flowering individuals. We were interested in the interactions between the flowering time groups; if there were gene flow between them and if so this was detrimental or advantageous. A spatially mixed population of early and late flowering individuals was studied using three microsatellite loci. We measured patterns in genetic differentiation and inferred occurrence of hybridisation and introgression. Variation in flowering time, fertility and relative and absolute fruit set was measured. The pattern of introgression between flowering-time groups differed between loci. In two of the three investigated loci, allele separation was distinct between early and late flowering plants and one genetically obvious hybrid was infertile. In the third locus, several alleles were shared between the two flowering time variants. The degree of introgression was associated to fruit set failure, which was higher in the late flowering plants and lower in early flowering plants. A small group of early flowering individuals with somewhat delayed flowering compared to the main group was genetically distinct and had lower relative and absolute fruit set. This group was not genetically intermediate, but rather constituting an independent group, with lower fruit set possibly caused by absence of pollinators. There seem to be a strong barrier against introgression into the late flowering group which is kept genetically distinct and less diverse. The early flowering group is diverse, includes two subgroups and seems to benefit from gene flow.     

Tetranuclear homoleptic copper and silver aryls: 2,4,6-Triethylphenylcopper and 2,4,6-triethylphenylsilver

The ethyl analogues of mesitylcopper and mesitylsilver, 2,4,6-triethylphenylcopper and 2,4,6-triethylphenylsilver, have been prepared and characterised by means of crystal structure determination. Three different compounds, [Cu₄(Et₃Ph)₄] · 2C₆H₅CH₃ (1), and , have thus been obtained by crystallisation from toluene or diethylether/tetrahydrofuran. All three show the square-planar metal core, most characteristic of homoleptic copper and silver aryls. The ordered (1) or disordered (2 and 3) solvent molecules are situated in the channels formed between the organometallic complexes, there being no strong directional interactions between the solvent and 2,4,6-triethylphenylcopper or 2,4,6-triethylphenylsilver.     

Salting the charged surface: pH and salt dependence of protein G B1 stability

This study shows significant effects of protein surface charges on stability and these effects are not eliminated by salt screening. The stability for a variant of protein G B1 domain was studied in the pH-range of 1.5-11 at low, 0.15 M, and 2 M salt. The variant has three mutations, T2Q, N8D, and N37D, to guarantee an intact covalent chain at all pH values. The stability of the protein shows distinct pH dependence with the highest stability close to the isoelectric point. The stability is pH-dependent at all three NaCl concentrations, indicating that interactions involving charged residues are important at all three conditions. We find that 2 M salt stabilizes the protein at low pH (protein net charge is +6 and total number of charges is 6) but not at high pH (net charge is or=18). Furthermore, 0.15 M salt slightly decreases the stability of the protein over the pH range. The results show that a net charge of the protein is destabilizing and indicate that proteins contain charges for reasons other than improved stability. Salt seems to reduce the electrostatic contributions to stability under conditions with few total charges, but cannot eliminate electrostatic effects in highly charged systems.     

Predicting the solvent accessibility of transmembrane residues from protein sequence

In this study, we propose a novel method to predict the solvent accessible surface areas of transmembrane residues. For both transmembrane alpha-helix and beta-barrel residues, the correlation coefficients between the predicted and observed accessible surface areas are around 0.65. On the basis of predicted accessible surface areas, residues exposed to the lipid environment or buried inside a protein can be identified by using certain cutoff thresholds. We have extensively examined our approach based on different definitions of accessible surface areas and a variety of sets of control parameters. Given that experimentally determining the structures of membrane proteins is very difficult and membrane proteins are actually abundant in nature, our approach is useful for theoretically modeling membrane protein tertiary structures, particularly for modeling the assembly of transmembrane domains. This approach can be used to annotate the membrane proteins in proteomes to provide extra structural and functional information.     

Experimental investigation of an optimization approach to microwave tomography

Microwave imaging is an interesting and growing research field with a number of medical applications. This paper is based on the first series of experimental results using an iterative gradient algorithm based on the finite difference time domain (FDTD) method and synthetic pulses. Using our method, the permittivity and conductivity of an object are reconstructed layer by layer by minimizing a functional consisting of the difference between the measured and calculated electric field surrounding the object. This is done by surrounding the object with a number of antennas which are all in turn transmitting and receiving. The dielectric profiles used in the calculations are then iteratively updated until the functional is minimized. Results are presented demonstrating the ability to detect metallic and dielectric material in air and water.     

How a lateralized brain supports symmetrical bimanual tasks

A large repertoire of natural object manipulation tasks require precisely coupled symmetrical opposing forces by both hands on a single object. We asked how the lateralized brain handles this basic problem of spatial and temporal coordination. We show that the brain consistently appoints one of the hands as prime actor while the other assists, but the choice of acting hand is flexible. When study participants control a cursor by manipulating a tool held freely between the hands, the left hand becomes prime actor if the cursor moves directionally with the left-hand forces, whereas the right hand primarily acts if it moves with the opposing right-hand forces. In neurophysiological (electromyography, transcranial magnetic brain stimulation) and functional magnetic resonance brain imaging experiments we demonstrate that changes in hand assignment parallels a midline shift of lateralized activity in distal hand muscles, corticospinal pathways, and primary sensorimotor and cerebellar cortical areas. We conclude that the two hands can readily exchange roles as dominant actor in bimanual tasks. Spatial relationships between hand forces and goal motions determine hand assignments rather than habitual handedness. Finally, flexible role assignment of the hands is manifest at multiple levels of the motor system, from cortical regions all the way down to particular muscles.     

Combining sequence-specific probes and DNA binding dyes in real-time PCR for specific nucleic acid quantification and melting curve analysis

Currently, in real-time PCR, one often has to choose between using a sequence-specific probe and a nonspecific double-stranded DNA (dsDNA) binding dye for the detection of amplified DNA products. The sequence-specific probe has the advantage that it only detects the targeted product, while the nonspecific dye has the advantage that melting curve analysis can be performed after completed amplification, which reveals what kind of products have been formed. Here we present a new strategy based on combining a sequence-specific probe and a nonspecific dye, BOXTO, in the same reaction, to take the advantage of both chemistries. We show that BOXTO can be used together with both TaqMan probes and locked nucleic acid (LNA) probes without interfering with the PCR. The probe signal reflect formation of target product, while melting curve analysis of the BOXTO signal reveals primer-dimer formation and the presence of any other anomalous products.