Tobamovirus evolution: gene overlaps, recombination, and taxonomic implications

Tobamoviruses, mostly isolated from solanaceous plants, may represent ancient virus lineages that have codiverged with their hosts. Recently completed nucleotide sequences of six nonsolanaceous tobamoviruses allowed assessment of the codivergence hypothesis and support a third subgroup within tobamoviruses. The genomic sequences of 12 tobamoviruses and the partial sequences of 11 others have been analyzed. Comparisons of the predicted protein sequences revealed three clusters of tobamoviruses, corresponding to those infecting solanaceous species (subgroup 1), those infecting cucurbits and legumes (subgroup 2), and those infecting crucifers. The orchid-infecting odontoglossum ringspot tobamovirus was associated with subgroup 1 genomes by its coat and movement protein sequences, but with the crucifer-pathogenic tobamoviruses by the remainder of its genome, suggesting that it is the progeny of a recombinant. For four of five genomic regions, subgroup 1 and 3 genomes were equidistant from a subgroup 2 genome chosen for comparison, suggesting uniform rates of evolution. A phylogenetic tree of plant families based on the tobamoviruses they harbor was congruent with that based on rubisco sequences but had a different root, suggesting that codivergence was tempered by rare events of viruses of one family colonizing another family. The proposed subgroup 3 viruses probably have an origin of virion assembly in the movement protein gene, a large (25-codon) overlap of movement and coat protein open reading frames, and a comparably shorter genome. Codon-position- dependent base compositions and codon prevalences suggested that the coat protein frame of the overlap region was ancestral. Bootstrapped parsimony analysis of the nucleotides in the overlap region and of the sequences translated from the -1 frame (the subgroup 3 movement protein frame) of this region produced trees inconsistent with those deduced from other regions. The results are consistent with a model in which a no or short overlap organization was ancestral. Despite encoding of subgroup 2 and 3 movement protein C-termini by nonhomologous nucleotides, weak similarities between their amino acid sequences suggested convergent sequence evolution.      

Opposite influence of medial preoptic D1 and D2 receptors on genital reflexes: implications for copulation.

Dopamine D1 and D2 receptors may synergize with or oppose each other's effects. We suggest that stimulation of D1 and D2 receptors in the medial preoptic area (MPOA) of male rats have opposing effects on genital reflexes. In Experiment 1 a D1 agonist injected into the MPOA increased the number of ex copula erections but decreased the number of seminal emissions. In Experiment 2 a D1 antagonist had the opposite effects (decreased erections and increased seminal emissions), as had a D2 agonist previously. We also suggest that D1 and D2 mechanisms in the MPOA have different thresholds of activation. In Experiment 3 a low dose of the mixed D1/D2 agonist apomorphine increased erections and anteroflexions, an effect blocked by the D1 antagonist. In Experiments 3 and 4 a high dose of apomorphine increased seminal emissions, an effect blocked by the D2 antagonist. Thus, low levels of dopaminergic stimulation may facilitate erections and anteroflexions (controlled by the parasympathetic system and striated muscles) via D1 receptors; higher or more prolonged stimulation may shift to seminal emission (controlled by the sympathetic system) via D2 receptors. This may explain the progression from erectile to ejaculatory mechanisms during copulation.     

Les environnements sédimentaires des gisements pré-acheuléens et acheuléens des wadis Akerdil et Bamouéré (Guelb er-Richât, Adrar, Mauritanie), une première approche

In the Mauritanian Adrar, the Guelb er-Richât and, in particular, the depression of its external ring are the location of rather exceptional Acheulian industry accumulations discovered by Théodore Monod. These sites may have originated from one or more non dated humid phases where seasonal water presence induced faunal and thus predator presence. Piedmont relief, foot slope rock flow and deltaic spreads attest, until the last humid Holocene, the permanence of particularly favourable sectors like upstream of Akerdil and Bamouéré wadis. Outcrops or chaos of Chinguetti quartzite sandstone have supplied the necessary raw material for tool confection; the second factor favouring the presence of these Acheulian sites. The rather difficult aim of the authors is first, to locate lithics in stratigraphic position and second, to establish a chronostratigraphy. Some first examples are presented.     

Évolution des caractères technologiques et typologiques des industries lithiques dans la stratigraphie de la Caune de l'Arago

The thick Quaternary deposits of the Caune de l’Arago (Pyrénées-Orientales, France) are dated to between 690 000 and 90 000 years old. At least fifteen different archeostratigraphical units have been identified within these deposits, each corresponding to distinct prehistoric occupations. Numerous stone tools made from several different rock types, have been discovered in each unit. The tools present specific characteristics concerning the choice of raw materials, the typology, and the technology used to produce them. Morpho-technological study of the different components of the assemblage contributes to a better understanding of the debitage methods used for their production. Each raw material is considered individually in order to ascertain its origin in the environment, its typological role and the technology applied during its exploitation. Defining production systems leads to the characterisation of the assemblages from each unit. When compared, they reveal common elements, as well as differences, suggesting evolutionary trends. Some observations are also made concerning the extent to which changing uses of the site may have influenced the general morphology of each assemblage, therefore taking into account exterior factors. Analysis of this rich stone tool assemblage helps to situate the Caune de l’Arago industry within the larger evolutionary context of the Lower Paleolithic in Mediterranean Europe.     

Sequence Analysis of Six Blood Pressure Candidate Regions in 4,178 Individuals: The Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Targeted Sequencing Study

Background

Genome-wide association studies (GWAS) identified multiple loci for blood pressure (BP) and hypertension. Six genes – ATP2B1, CACNB2, CYP17A1, JAG1, PLEKHA7, and SH2B3 – were evaluated for sequence variation with large effects on systolic blood pressure (SBP), diastolic blood pressure (DBP), pulse pressure (PP), and mean arterial pressure (MAP).

Methods and Results

Targeted genomic sequence was determined in 4,178 European ancestry participants from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium. Common variants (≥50 minor allele copies) were evaluated individually and rare variants (minor allele frequency, MAF≤1%) were aggregated by locus. 464 common variants were identified across the 6 genes. An upstream CYP17A1 variant, rs11191416 (MAF = 0.09), was the most significant association for SBP (P = 0.0005); however the association was attenuated (P = 0.0469) after conditioning on the GWAS index single nucleotide polymorphism (SNP). A PLEKHA7 intronic variant was the strongest DBP association (rs12806040, MAF = 0.007, P = 0.0006) and was not in LD (r² = 0.01) with the GWAS SNP. A CACNB2 intronic SNP, rs1571787, was the most significant association with PP (MAF = 0.27, P = 0.0003), but was not independent from the GWAS SNP (r² = 0.34). Three variants (rs6163 and rs743572 in the CYP17A1 region and rs112467382 in PLEKHA7) were associated with BP traits (P<0.001). Rare variation, aggregately assessed in the 6 regions, was not significantly associated with BP measures.

Conclusion

Six targeted gene regions, previously identified by GWAS, did not harbor novel variation with large effects on BP in this sample.     

Conclusion. Bilan des recherches interdisciplinaires effectuées sur le site de l’Homo erectus de Denizli,Kocabaş, Bassin de Denizli,Anatolie, Turquie. L’Homo erectus aux portes de l’Europe

The study of the site of Kocaba?, which yielded an archaic Homo erectus skullcap, was undertaken in 2011 and 2012, at the request of Professor Mehmet Cihat Alçiçek. This interdisciplinary French–Turkish research programme comprised the geochronological, magnetostratigraphic, biochronological and paleoenvironmental study of the site and the paleoanthropological study of the skullcap itself. The association of large mammals enabled us to attribute the travertine formations bearing the skullcap to the second part of the Upper Pleistocene, and more specifically to between 1.5 and 1.2 million years, because of the disappearance or appearance of certain species. This biochronological age is confirmed by the paleomagnetism study, which places the travertines bearing the skullcap in a period of reversed polarity, underlying a normal polarity formation, which could be attributed to the Cobb Mountain paleomagnetic excursion, dated to 1,194,000 years. The dating of these fauna by the ²⁶Al/¹⁰Be cosmogenic nuclide method by Anne-Elisabeth Lebatard yielded an age older than 1.22 Ma and more recent than 1.5 Ma. The Hominid skullcap from this formation can be attributed to a Homo erectus, slightly more evolved than those of Homo ergaster KNM-ER 3733 (1.78 Ma) and KNM-ER 15,000 (1.5 Ma), similar to that of Daka (Bouri), which is about a million years old and older than the Bodo fossil (estimated at 600,000 years) and Kabwe (between 300,000 and120,000 years). The archaic Homo erectus skullcap from Kocaba?, referred to as Denizli Man, proves that Homo erectus was already present in Anatolia, at the crossroads of Africa, Asia and Europe, a little more than 1.2 million years ago.