Phylogenetic reconstruction of Aegilops section Sitopsis and the evolution of tandem repeats in the diploids and derived wheat polyploids.

The evolution of 2 tandemly repeated sequences Spelt1 and Spelt52 was studied in Triticum species representing 2 evolutionary lineages of wheat and in Aegilops sect. Sitopsis, putative donors of their B/G genomes. Using fluorescence in situ hybridization we observed considerable polymorphisms in the hybridization patterns of Spelt1 and Spelt52 repeats between and within Triticum and Aegilops species. Between 2 and 28 subtelomeric sites of Spelt1 probe were detected in Ae. speltoidies, depending on accession. From 8 to 12 Spelt1 subtelomeric sites were observed in species of Timopheevi group (GAt genome), whereas the number of signals in emmer/aestivum accessions was significantly less (from 0 to 6). Hybridization patterns of Spelt52 in Ae. speltoides, Ae. longissima, and Ae. sharonensis were species specific. Subtelomeric sites of Spelt52 repeat were detected only in T. araraticum (T. timopheevii), and their number and chromosomal location varied between accessions. Superimposing copy number data onto our phylogenetic scheme constructed from RAPD data suggests 2 major independent amplifications of Spelt52 and 1 of Spelt1 repeats in Aegilops divergence. It is likely that the Spelt1 amplification took place in the ancient Ae. speltoides before the divergence of polyploid wheats. The Spelt52 repeat was probably amplified in the lineage of Ae. speltoides prior to divergence of the allopolyploid T. timopheevii but after the divergence of T. durum. In a separate amplification event, Spelt52 copy number expanded in the common ancestor of Ae. longissima and Ae. sharonensis.     

TNF-α potentiates lysophosphatidic acid-induced COX-2 expression via PKD in human colonic myofibroblasts

The myofibroblast (MFB) has recently been identified as an important mediator of tumor necrosis factor-α (TNF-α)-associated colitis and cancer, but the mechanism(s) involved remains incompletely understood. Here, we show that treatment of 18Co cells, a model of human colonic MFBs, with TNF-α and lysophosphatidic acid (LPA) induced striking synergistic cyclooxygenase-2 (COX-2) protein expression and production of PGE(2). This effect was prevented by the LPA(1) receptor antagonist Ki16425, the G(iα)-specific inhibitor pertussis toxin, and by the preferential protein kinase (PK) C inhibitors GF109203X and Go6983. As a known downstream target of LPA and PKC, we tested whether PKD, recently implicated in the regulation of COX-2 expression in MFB, was involved in this response. TNF-α, while having no detectable effect on the activation of PKD when added alone, augmented PKD activation stimulated by LPA, as measured by PKD autophosphorylation at Ser(910). LPA-induced PKD activation was also inhibited by Ki16425, pertussis toxin, GF109203X, and Go6983. Transfection of 18Co cells with short interfering RNA targeting PKD completely inhibited the synergistic increase in COX-2 protein, demonstrating a critical role of PKD in this response. Our results imply that cross talk between TNF-α and LPA results in the amplification of COX-2 protein expression via a conserved PKD-dependent signaling pathway that appears to involve the LPA(1) receptor and the G protein G(iα). PKD plays a critical role in the expression of COX-2 in human colonic MFBs and may contribute to an inflammatory microenvironment that promotes tumor growth.     

Nasal and Oral Calls in Juvenile Goitred Gazelles (Gazella subgutturosa) and their Potential to Encode Sex and Identity

Like many other gazelles, goitred gazelles (Gazella subgutturosa) are capable of calling either through the nose or through the open mouth. In particular, juvenile goitred gazelles provide a convenient model for contrasting acoustic characteristics of nasal and oral calls, and for estimating their communicative functions. In this study, acoustic variables (formants, fundamental frequency, duration and power quartiles) of 480 oral and 483 nasal calls, recorded from 20 (9 male, 11 female) individually identified captive juvenile goitred gazelles, were examined for their potential to encode sex and identity of the caller. Discriminant function analysis revealed an equally high potential of oral and nasal calls to encode sex, whereas encoding the individual identity was significantly more accurate for oral calls. Sex was encoded exclusively in formants, whilst individual identity was encoded in a combination of all investigated variables. No correlation was found between body mass and values of any acoustic variable. Analyses controlling for age and sex revealed higher average values for all investigated variables of oral calls compared to nasal calls. We discuss the results in relation to the source‐filter theory, mother–offspring communication and production mechanisms of nasal and oral calls in mammals.     

High abundances of aerobic anoxygenic phototrophs in saline steppe lakes

We studied the distribution of anoxygenic phototrophs in 23 steppe lakes in the Transbaikal region (Russia), in Uzbekistan (Central Asia) and in the Crimean peninsula (Ukraine). The lakes varied in their mineral content and composition (salinities from 0.2 to 300 g L(-1) ). The Transbaikal lakes were alkaline (pH>9), with high amounts of soda. The Uzbek and Crimean lakes were more pH neutral, frequently with high amounts of sulfates. The presence of anoxygenic phototrophs was registered by infrared epifluorescence microscopy, infrared fluorometry and pigment analyses. In mostly shallow, fully oxic lakes, the anoxygenic phototrophs represented 7-65% of the total prokaryotes, with the maxima observed in Transbaikal soda lakes Gorbunka (32%), Khilganta (65%), Zanday (58%) and Zun-Kholvo (46%). Some of the lakes contained over 1 μg bacteriochlorophyll L(-1) . In contrast, only small amounts of anoxygenic phototrophs were present in highly mineralized lakes (>100 g total salts L(-1) ); Borzinskoe, Tsagan-Nur (Transbaikal), Staroe (Crimea) and in the residual part of the south-west Aral Sea (Uzbekistan). The oxic environment and the specific diurnal changes of bacteriochlorophyll concentration observed suggest that the phototrophic community was mostly composed of aerobic anoxygenic phototrophs. The high abundances and bacteriochlorophyll concentrations point to an important role of aerobic anoxygenic phototrophs in the habitats studied.     

Disruption of shape complementarity in the ribosomal protein L1–RNA contact region does not hinder specific recognition of the RNA target site

The formation of a specific and stable complex between two (macro)molecules implies complementary contact surface regions. We used ribosomal protein L1, which specifically binds a target site on 23S rRNA, to study the influence of surface modifications on the protein?RNA affinity. The threonine residue in the universally conserved triad Thr?Met?Gly significant for RNA recognition and binding was substituted by phenylalanine, valine and alanine, respectively. The crystal structure of the mutant Thr217Val of the isolated domain I of L1 from Thermus thermophilus (TthL1) was determined. This structure and that of two other mutants, which had been determined earlier, were analysed and compared with the structure of the wild type L1 proteins. The influence of structural changes in the mutant L1 proteins on their affinity for the specific 23S rRNA fragment was tested by kinetic experiments using surface plasmon resonance (SPR) biosensor analysis. Association rate constants undergo minor changes, whereas dissociation rate constants displayed significantly higher values in comparison with that for the wild type protein. The analysed L1 mutants recognize the specific RNA target site, but the mutant L1?23S rRNA complexes are less stable compared to the wild type complexes. Copyright © 2010 John Wiley & Sons, Ltd.     

Pathways of transport protein evolution: recent advances

We herein report recent advances in our understanding of transport protein evolution. Numerous families of complex transmembrane transport proteins are believed to have arisen from short channel-forming amphipathic or hydrophobic peptides by various types of intragenic duplication events. Distinct pathways distinguish families, demonstrating independent origins for some, and allowing assignment of others to superfamilies. Some families have diversified in topology, whereas others have remained uniform. An example of 'retroevolution' was discovered where a more complex carrier gave rise to a structurally and functionally simpler channel. The results described in this review article expand our understanding of protein evolution.     

Exploring the binding dynamics of BAR proteins

We used a continuum model based on the Helfrich free energy to investigate the binding dynamics of a lipid bilayer to a BAR domain surface of a crescent-like shape of positive (e.g. I-BAR shape) or negative (e.g. F-BAR shape) intrinsic curvature. According to structural data, it has been suggested that negatively charged membrane lipids are bound to positively charged amino acids at the binding interface of BAR proteins, contributing a negative binding energy to the system free energy. In addition, the cone-like shape of negatively charged lipids on the inner side of a cell membrane might contribute a positive intrinsic curvature, facilitating the initial bending towards the crescent-like shape of the BAR domain. In the present study, we hypothesize that in the limit of a rigid BAR domain shape, the negative binding energy and the coupling between the intrinsic curvature of negatively charged lipids and the membrane curvature drive the bending of the membrane. To estimate the binding energy, the electric potential at the charged surface of a BAR domain was calculated using the Langevin-Bikerman equation. Results of numerical simulations reveal that the binding energy is important for the initial instability (i.e. bending of a membrane), while the coupling between the intrinsic shapes of lipids and membrane curvature could be crucial for the curvature-dependent aggregation of negatively charged lipids near the surface of the BAR domain. In the discussion, we suggest novel experiments using patch clamp techniques to analyze the binding dynamics of BAR proteins, as well as the possible role of BAR proteins in the fusion pore stability of exovesicles.     

Nde1-mediated inhibition of ciliogenesis affects cell cycle re-entry

The primary cilium is an antenna-like organelle that is dynamically regulated during the cell cycle. Ciliogenesis is initiated as cells enter quiescence, whereas resorption of the cilium precedes mitosis. The mechanisms coordinating ciliogenesis with the cell cycle are unknown. Here we identify the centrosomal protein Nde1 (nuclear distribution gene E homologue 1) as a negative regulator of ciliary length. Nde1 is expressed at high levels in mitosis, low levels in quiescence and localizes at the mother centriole, which nucleates the primary cilium. Cells depleted of Nde1 have longer cilia and a delay in cell cycle re-entry that correlates with ciliary length. Knockdown of Nde1 in zebrafish embryos results in increased ciliary length, suppression of cell division, reduction of the number of cells forming the Kupffer's vesicle and left-right patterning defects. These data suggest that Nde1 is an integral component of a network coordinating ciliary length with cell cycle progression and have implications for understanding the transition from a quiescent to a proliferative state.