FTIR studies of phytochrome photoreactions reveal the C=O bands of the chromophore: consequences for its protonation states, conformation, and protein interaction.

The molecular changes of phytochrome during red --> far-red and reverse photoreactions have been monitored by static infrared difference spectroscopy using the recombinant 65 kDa N-terminal fragment assembled with a chromophore chemically modified at ring D or with a chromophore isotopically labeled with (18)O at the carbonyl group of ring A. This allows the identification of the C=O stretching vibrations of rings D and A. We exclude the formation of an iminoether in Pfr. The positions of both these modes show that the chromophore always remains protonated. The upshift of the C=O stretch of ring D in the first photoproducts is explained by a twisted methine bridge connecting rings C and D. The changes in the vibrational pattern during the red --> far-red conversion show that the backreaction is not just the reversal of the forward reaction. The infrared difference spectra of the fragment deviate very little from those of the full-length protein. The differences which are related to the lack of the C-terminal half of the protein constituting the signaling domain are possibly important for the understanding of the signaling mechanism.     

Molecules,morphometrics and new fossils provide an integrated view of the evolutionary history of Rhinopomatidae (Mammalia: Chiroptera)

Background  

The Rhinopomatidae, traditionally considered to be one of the most ancient chiropteran clades, remains one of the least known groups of Rhinolophoidea. No relevant fossil record is available for this family. Whereas there have been extensive radiations in related families Rhinolophidae and Hipposideridae, there are only a few species in the Rhinopomatidae and their phylogenetic relationship and status are not fully understood.     

A Neural Mechanism for Time-Window Separation Resolves Ambiguity of Adaptive Coding

The senses of animals are confronted with changing environments and different contexts. Neural adaptation is one important tool to adjust sensitivity to varying intensity ranges. For instance, in a quiet night outdoors, our hearing is more sensitive than when we are confronted with the plurality of sounds in a large city during the day. However, adaptation also removes available information on absolute sound levels and may thus cause ambiguity. Experimental data on the trade-off between benefits and loss through adaptation is scarce and very few mechanisms have been proposed to resolve it. We present an example where adaptation is beneficial for one task—namely, the reliable encoding of the pattern of an acoustic signal—but detrimental for another—the localization of the same acoustic stimulus. With a combination of neurophysiological data, modeling, and behavioral tests, we show that adaptation in the periphery of the auditory pathway of grasshoppers enables intensity-invariant coding of amplitude modulations, but at the same time, degrades information available for sound localization. We demonstrate how focusing the response of localization neurons to the onset of relevant signals separates processing of localization and pattern information temporally. In this way, the ambiguity of adaptive coding can be circumvented and both absolute and relative levels can be processed using the same set of peripheral neurons.     

Evolutionary Modeling and Prediction of Non-Coding RNAs in Drosophila

We performed benchmarks of phylogenetic grammar-based ncRNA gene prediction, experimenting with eight different models of structural evolution and two different programs for genome alignment. We evaluated our models using alignments of twelve Drosophila genomes. We find that ncRNA prediction performance can vary greatly between different gene predictors and subfamilies of ncRNA gene. Our estimates for false positive rates are based on simulations which preserve local islands of conservation; using these simulations, we predict a higher rate of false positives than previous computational ncRNA screens have reported. Using one of the tested prediction grammars, we provide an updated set of ncRNA predictions for D. melanogaster and compare them to previously-published predictions and experimental data. Many of our predictions show correlations with protein-coding genes. We found significant depletion of intergenic predictions near the 3′ end of coding regions and furthermore depletion of predictions in the first intron of protein-coding genes. Some of our predictions are colocated with larger putative unannotated genes: for example, 17 of our predictions showing homology to the RFAM family snoR28 appear in a tandem array on the X chromosome; the 4.5 Kbp spanned by the predicted tandem array is contained within a FlyBase-annotated cDNA.     

Models of the bis-histidine-coordinated ferricytochromes: Mössbauer and EPR spectroscopic studies of low-spin iron(III) tetrapyrroles of various electronic ground states and axial ligand orientations

The EPR and magnetic Mössbauer spectra of a series of axial ligand complexes of tetrakis(2,6-dimethoxyphenyl)porphyrinatoiron(III), [(2,6-(OMe)₂)₄TPPFeL₂]⁺, where L=N-methylimidazole, 2-methylimidazole, or 4-(dimethylamino)pyridine, of one axial ligand complex of tetraphenylporphyrin, the bis(4-cyanopyridine) complex [TPPFe(4-CNPy)₂]⁺, and of one axial ligand complex of tetraphenylchlorin, [TPCFe(ImH)₂]⁺, where ImH=imidazole, have been investigated and compared to those of low-spin Fe(III) porphyrinates and ferriheme proteins reported in the literature. On the basis of this and previous complementary spectroscopic investigations, three types of complexes have been identified: those having (d_xy)²(d_xz,d_yz)³ electronic ground states with axial ligands aligned in perpendicular planes (Type I), those having (d_xy)²(d_xz,d_yz)³ electronic ground states with axial ligands aligned in parallel planes (Type II), and those having the novel (d_xz,d_yz)⁴(d_xy)¹ electronic ground state (Type III). A subset of the latter type, with planar axial ligands aligned parallel to each other or strong macrocycle asymmetry that yield rhombic EPR spectra, cannot be created using the porphyrinate ligand. Type I centers are characterized by "large g_max" EPR spectra with g>3.2 and well-resolved, widely spread magnetic Mössbauer spectra having A_zz/g_NN>680 kG, with A_xx negative in sign but much smaller in magnitude than A_zz, while Type II centers have well-resolved rhombic EPR spectra with g_zz=2.4–3.1 and also less-resolved magnetic Mössbauer spectra, and usually have A_zz/g_NN in the range of 440–660 kG (but in certain cases as small as 180 kG) and A_xx again negative in sign but only somewhat smaller (but occasionally larger in magnitude) than A_zz, and Type III centers have axial EPR spectra with g_┴2.6 or smaller and g_║<1.0–1.95, but often not resolved, and less-resolved magnetic Mössbauer spectra having A_zz/g_NN in the range of 270–400 kG, and A_xx again negative in sign but much smaller in magnitude than A_zz. An exception to this rule is [TPPFe(4-CNPy)₂]⁺, which has A_xx/g_NN=–565 kG, A_yy/g_NN=629 kG, and A_zz/g_NN=4 kG. A subset of Type II complexes (Type II) have rhombicities (V/) much greater than 0.67 and A_zz/g_NN ranging from 320 to 170 kG, with A_xx also negative but with the magnitude of A_xx significantly larger than that of A_zz. These classifications are also observed for a variety of ferriheme proteins, and they lead to linear correlations between A_zz and either A_xx, g_zz, or V/ for Types I and II (but not for A_zz versus V/ for Type II). Not enough data are yet available on Type III complexes to determine what, if any, correlations may be observed.Abbreviations CCP cytochrome c peroxidase - 4-CNPy 4-cyanopyridine - cyt cytochrome - EFG electric field gradient - ESEEM electron spin echo envelope modulation - ImH imidazole - Mb myoglobin - MCD magnetic circular dichroism - 2-MeImH 2-methylimidazole - N-MeIm N-methylimidazole - 3NH₂PzH 3-aminopyrazole - 4-NMe₂Py 4-(dimethylamino)pyridine - [2,6-(OMe)₂]₄TPP dianion of tetrakis(meso-2,6-dimethoxyphenyl)porphyrin - OEiBC dianion of octaethylisobacteriochlorin - OEP dianion of octaethylporphyrin - PPIX dianion of protoporphyrin IX - Py pyridine - TMP dianion of meso-tetramesitylporphyrin - TPC dianion of meso-tetraphenylchlorin - TPP dianion of meso-tetraphenylporphyrin - 2,6-XylylNC 2,6-xylyl isocyanide     

Isolation and characterization of rabbit caecal pectinolytic bacteria

Two hundred and thirty colonies from the caecal contents of six rabbits were picked up and, after a 2-d incubation, were microscopically characterized using Gram staining. Large Gram-negative (34%) and small Gram-negative (30%) irregular rods, Gram-negative (27%) and Gram-positive (8%) cocci were found. Eleven isolates (Bacteroides ovatus (6 strains),B. thetaiotamicron, B. caccae, B. stercoris, B. capillosus andCapnocytophaga ochracea) were identified using commercial tests for measuring their catalase activity, metabolite production,etc., and testing their growth in 20% bile. Bacteria belonging to the genusBacteroides were demonstrated to be the principal pectinolytic organisms in the rabbit caecum.     

The European acamprosate trials: Conclusions for research and therapy

In an excellent methodological approach, the European acamprosate study project showed that acamprosate increases sobriety times. In one randomized prospective study (n = 260) comparing acamprosate and placebo, with a 1-year treatment phase and 1-year follow-up phase, the authors found that acamprosate is effective only in Lesch type I and type II patients. To investigate the possible influence of diagnostic subgrouping, we applied the Lesch typology in a co-work with the main researchers of the UK study. The UK results concerning acamprosate's effects in the types do not mirror the Vienna results, but the numbers of type I and type II patients, retrospectively found as included in the UK centers, were too small for any conclusions. The distribution of the types points to the fact that too many type III and IV patients had been included to give acamprosate the chance to be effective. Following our typology and also these studies, we developed special treatment approaches. For relapse prevention studies, the cumulative abstinence duration together with the Lesch typology seems to be promising.     

Mitochondrial phylogeography of the long-eared bats (Plecotus) in the Mediterranean Palaearctic and Atlantic Islands

Long-eared bats of the genus Plecotus are widespread and common over most of the western Palaearctic. Based on recent molecular evidence, they proved to represent a complex of several cryptic species, with three new species being described from Europe in 2002. Evolutionary relationships among the different lineages are still fragmentary because of the limited geographic coverage of previous studies. Here we analyze Plecotus mitochondrial DNA sequences from the entire Mediterranean region and Atlantic Islands. Phylogenetic reconstructions group these western Palaearctic Plecotus into two major clades which split at least 5 Myr ago and that are each subdivided into further subgroups. An 'auritus group' includes the traditional P. auritus species and its sister taxon P. macrobullaris (=P. alpinus) plus related specimens from the Middle East. P. auritus and P. macrobullaris have broadly overlapping distributions in Europe, although the latter is apparently more restricted to mountain ranges. The other major clade, the 'austriacus group,' includes the European species P. austriacus and at least two other related taxa from North Africa (including P. teneriffae from the Canary Islands), the Balkans and Anatolia (P. kolombatovici). The sister species of this 'austriacus group' is P. balensis, an Ethiopian endemic. Phylogenetic reconstructions further suggest that P. austriacus reached Madeira during its relatively recent westward expansion through Europe, while the Canary Islands were colonized by a North African ancestor. Although colonization of the two groups of Atlantic Islands by Plecotus bats followed very distinct routes, neither involved lineages from the 'auritus group.' Furthermore, the Strait of Gibraltar perfectly segregates the distinct lineages, which confirms its key role as a geographic barrier. This study also stresses the biogeographical importance of the Mediterranean region, and particularly of North Africa, in understanding the evolution of the western Palaearctic biotas.