Bird mitochondrial gene order: insight from 3 warbler mitochondrial genomes

Two main gene orders exist in birds: the ancestral gene order and the remnant control region (CR) 2 gene order. These gene orders differ by the presence of 1 or 2 copies of the CR, respectively. Among songbirds, Oscines were thought to follow the ancestral gene order, with the exception of the lyrebird and Phylloscopus warblers. Here, we determined the complete mitochondrial genome sequence of 3 non-Phylloscopus warblers species and found that the blackcap (Sylvia atricapilla) and the reed warbler (Acrocephalus scirpaceus) have 2 almost identical copies of the CR, whereas the eastern orphean warbler (Sylvia crassirostris) follows the remnant CR 2 gene order. Our results contradict previous studies suggesting that Acrocephalus and most sylvioid warblers exhibit the ancestral gene order. We were able to trace this contradiction to a misidentification of gene order from polymerase chain reaction length determination. We thus suggest that passerine gene order evolution needs to be revised.     

Rational design of a CD4 mimic that inhibits HIV-1 entry and exposes cryptic neutralization epitopes

The conserved surfaces of the human immunodeficiency virus (HIV)-1 envelope involved in receptor binding represent potential targets for the development of entry inhibitors and neutralizing antibodies. Using structural information on a CD4-gp120-17b antibody complex, we have designed a 27-amino acid CD4 mimic, CD4M33, that presents optimal interactions with gp120 and binds to viral particles and diverse HIV-1 envelopes with CD4-like affinity. This mini-CD4 inhibits infection of both immortalized and primary cells by HIV-1, including primary patient isolates that are generally resistant to inhibition by soluble CD4. Furthermore, CD4M33 possesses functional properties of CD4, including the ability to unmask conserved neutralization epitopes of gp120 that are cryptic on the unbound glycoprotein. CD4M33 is a prototype of inhibitors of HIV-1 entry and, in complex with envelope proteins, a potential component of vaccine formulations, or a molecular target in phage display technology to develop broad-spectrum neutralizing antibodies.     

Mothering influences the distribution of activity in young domestic chicks

The aim of this study was to determine whether the presence of a maternal hen influences the quality, quantity, and distribution of activity in young chicks. Brooded and nonbrooded chicks were observed during the entire light phase when they were 4 d of age. Our results revealed that although both brooded and nonbrooded chicks expressed the same behavioral items and in quite the same quantity, activity bouts were much longer in brooded chicks. However, only brooded chicks presented a high level of ultradian rhythmicity. Moreover, the brooded chicks made greater use of the space. The presence and the behavior of maternal hens appeared to provide structuring factors for the expression of the chicks' behavior.     

Osteopontin, a multi-faceted molecule

Osteopontin (OPN) was initially isolated from bovine bone cortex, as a complex syalilated phospho-glyco-protein of around 60 kDa, with many postranslational modifications. It has been long considered a structural bone protein linking bone cells to the bone extracellular matrix (osteo : bone, pontin : bridge). It has been cloned for the first time in 1986. Since then, it was established that it is part of a protein family called SIBLINGs, which genes share common expression in bone and tooth, and encode among others a RGD motif. OPN is an intracellular as well as secreted protein, which binds to multiple organic or mineral ligands, like the integrin receptor alphaVbeta3, CD44, factor H and hydroxyapatite, depending on its final configuration (phosphorylation state). Pleiotropic functions of osteopontin have been demonstrated, and the osteopontin knock out phenotype in mice gave some new insight on the implication of the molecule in vivo. Osteopontin inhibits mineralization in bone and urine. Besides, it is a strong chemoattractive and proinflammatory molecule, implicated in tumors, like breast or prostate cancers, and in the defense against various infectious agents like tuberculosis, listeria or herpes. More recently, its key implication in TH1 mediated autoimmune diseases like multiple sclerosis and its animal model experimental autoimmune encephalomyelitis has been demonstrated. Osteopontin is a valuable therapeutic target in the animal model, and a biological tool correlating with clinical disease activity in humans. Structural, functional and pathological aspects of osteopontin are reviewed, as well as the osteopontin deficient phenotype in mouse.     

Stromal cell-derived factor-1 (SDF-1) expression in embryonic mouse cerebral cortex starts in the intermediate zone close to the pallial-subpallial boundary and extends progressively towards the cortical hem

We describe the onset and the expansion of stromal cell-derived factor 1 (SDF-1) expression in the intermediate zone of embryonic mouse cerebral cortex between embryonic days (E)11.5 and 18.5, and on postnatal day 1. Using in situ hybridisation with a digoxigenin-labeled probe, SDF-1 mRNA was detectable by E 12.5 in a small area of the intermediate zone just dorsal to the pallial-subpallial boundary. During the following days, SDF-1 expression extended towards the dorso-lateral pallium, and then the hippocampus and cortical hem. The position of the SDF-1 positive cells within the intermediate zone was closely correlated with the stream of tangentially migrating cells carrying the polysialylated form of neural cell adhesion molecule (PSA-NCAM). However, whereas these cells form a ventro-dorsal stream passing from the subpallium into the pallium, SDF-1 was not detectable on the ventral side of the pallial-subpallial boundary at any of the developmental stages studied. By E 16.5, the intensity of SDF-1 hybridisation signal in the intermediate zone decreased, to become undetectable by E 18.5.     

Improvement of the fungal enzyme pyranose 2-oxidase using protein engineering

Native pyranose 2-oxidase (P2Ox) was purified from Peniophora sp. and characterized. To improve its catalytic efficiencies and stabilities by protein engineering, we cloned and expressed the P2Ox gene in Escherichia coli and received active, fully flavinylated recombinant P2OxA. Selenomethionine-labeled P2OxA was used for X-ray analysis and the resulting crystal structure enabled the rational design using variant P2OxA1 with the substitution E542K as template. Besides increased thermal and pH stabilities this variant showed improved catalytic efficiencies (k(cat)/K(m)) for the main substrates. A new variant, P2OxA2H, with an additional substitution T158A and a C-terminal His(6)-tag exhibited significantly decreased apparent K(m) values for D-glucose (0.47 mM), l-sorbose (1.79 mM), and D-xylose (1.35 mM). Compared to native P2Ox, the catalytic efficiencies were substantially improved for D-glucose (230-fold), L-sorbose (874-fold), and D-xylose (1751-fold). This P2Ox variant was used for the bioconversion of L-sorbose under O(2)-saturation in a molar scale. The structure-activity relationships of the amino acid substitutions were analyzed by modelling of the mutated P2Ox structures. Molecular docking calculations of various carbohydrates into the crystal structure of P2OxA and the analysis of the protein-ligand interactions in the docked complexes enabled us to explain the substrate specificity of the enzyme by a conserved hydrogen bond pattern which is formed between the protein and all substrates.     

Arrival and diversification of caviomorph rodents and platyrrhine primates in South America

Platyrrhine primates and caviomorph rodents are clades of mammals that colonized South America during its period of isolation from the other continents, between 100 and 3 million years ago (Mya). Until now, no molecular study investigated the timing of the South American colonization by these two lineages with the same molecular data set. Using sequences from three nuclear genes (ADRA2B, vWF, and IRBP, both separate and combined) from 60 species, and eight fossil calibration constraints, we estimated the times of origin and diversification of platyrrhines and caviomorphs via a Bayesian relaxed molecular clock approach. To account for the possible effect of an accelerated rate of evolution of the IRBP gene along the branch leading to the anthropoids, we performed the datings with and without IRBP (3768 sites and 2469 sites, respectively). The time window for the colonization of South America by primates and by rodents is demarcated by the dates of origin (upper bound) and radiation (lower bound) of platyrrhines and caviomorphs. According to this approach, platyrrhine primates colonized South America between 37.0 +/- 3.0 Mya (or 38.9 +/- 4.0 Mya without IRBP) and 16.8 +/- 2.3 (or 20.1 +/- 3.3) Mya, and caviomorph rodents between 45.4 +/- 4.1 (or 43.7 +/- 4.8) Mya and 36.7 +/- 3.7 (or 35.8 +/- 4.3) Mya. Considering both the fossil record and these molecular datings, the favored scenarios are a trans-Atlantic migration of primates from Africa at the end of the Eocene or beginning of the Oligocene, and a colonization of South America by rodents during the Middle or Late Eocene. Based on our nuclear DNA data, we cannot rule out the possibility of a concomitant arrival of primates and rodents in South America. The caviomorphs radiated soon after their arrival, before the Oligocene glaciations, and these early caviomorph lineages persisted until the present. By contrast, few platyrrhine fossils are known in the Oligocene, and the present-day taxa are the result of a quite recent, Early Miocene diversification.     

The nature of lemming cycles on Wrangel: an island without small mustelids

Lemming cycles are a key process in the functioning of tundra ecosystems. Although it is agreed that trophic interactions are important in causing the cycles, the actual mechanism is disputed. Some researchers attribute a major role to predation by small mustelids such as stoats and least weasels. Here we present a 40-year time series of lemming dynamics from Wrangel Island and show statistically that lemmings do exhibit population cycles in the absence of small mustelids. The observed density fluctuations differed, however, from those observed elsewhere, with long cycles and possibly higher densities of lemmings during the low phase. These differences in the shape of the population cycles may be related to the unique species assemblage of Wrangel Island, where arctic foxes are the only year-round resident lemming predator, and to the high diversity of landscapes, microclimatic conditions, and plants on the island. Both spectral analysis and wavelet analysis show a change in period length from five?years in the 1970s to nearly eight?years in the 1990s and 2000s. This change in dynamics coincides with reports of dampening or fading out of lemming cycles that have been observed in several regions of the Arctic in recent decades. As in the other cases, the changed lemming dynamics on Wrangel Island may be related to ground icing in winter, which could delay peak years.