Éditeur(s) : HAL CCSD Society of Economic Geologists
Résumé : International audience
The ~8-Moz Sadiola Hill gold deposit is located in the Kédougou-Kénieba inlier, a window of deformed ca. 2200 to 2050 Ma rocks that crop out in eastern Senegal and western Mali. The geology of the inlier differs from other Paleoproterozoic granite-greenstone belts and sedimentary basins by the abundance of carbonate rocks. The Sadiola Hill gold deposit occurs within 3 km of the Senegal-Mali shear zone, and country rocks in the region have undergone polycyclic deformation. The lithostratigraphy of the open pit consists of impure limestones overlain by younger sequences of detrital sedimentary rocks, which include arenite, wacke, and siltstone. The sedimentary rocks have been subjected to regional greenschist-facies metamorphism and have been intruded by multiple generations of synkinematic, calc-alkaline stocks and dikes. The bulk of the ore is hosted within a N-S- to NNW-trending, 10- to 50-m-wide, brittle-ductile dilational shear zone defined as the Sadiola shear zone. Gold lodes also occur along an array of steep NNE-trending shear zones. Geometric and kinematic analyses indicate that the ore-hosting structures were undergoing sinistral displacement at the time of mineralization, locally defined as the D3s NNW-SSE-shortening event. Hydrothermal alteration is polyphase and includes an early high-temperature calc-silicate phase (i.e., porphyroblastic growth of actinolite-tremolite) followed by a potassic phase (i.e., biotite-calcite-quartz ± K-feldspar-tourmaline-actinolite) that was synchronous with ore mineral deposition. Paragenetic studies reveal a multistage ore development that includes an As-rich sulfide stage, followed by an Au-Sb stage. The ore is associated with a metal enrichment suite of Au-As-Sb ± Cu-Fe-W-Mo-Ag-Bi-Zn-Pb-Te. The Sadiola Hill deposit shares a similar relative timing and structural setting to that of other world-class orogenic gold systems in the West African craton (e.g., Ashanti, Loulo), with gold deposition occurring during a period of transcurrent tectonics, after the cessation of region-wide compressional deformation. The high-temperature paragenesis at Sadiola Hill is atypical of gold mineralization in the craton and indicates that the late Eburnean tectono-magmatic activity between ca. 2080 and 2060 Ma played an important role in the dynamics of hydrothermal fluid circulation along the Senegal-Mali shear zone.
ISSN: 0361-0128

hal-01583358
https://hal.archives-ouvertes.fr/hal-01583358
DOI : 10.2113/econgeo.112.1.23

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
Bruggemann, J.H. (2016). Phylogenetic relationships within Aglaopheniidae (Cnidaria, Hydrozoa) reveal unexpected generic diversity. — Zoologica Scripta, 45, 103–114. Morphology can be misleading in the representation of phylogenetic relationships, especially in simple organisms like cnidarians and particularly in hydrozoans. These suspension feeders are widely distributed in many marine ecosystems, and the family Aglaopheniidae Marktanner-Turneretscher, 1890 is among the most diverse and visible, especially on tropical coral reefs. The taxonomy of this family is based on morphological characters with emphasis on reproductive structures for the identification of genera. This study is the most comprehensive molecular phylogeny of the Aglaopheniidae to date, including six genera and 38 species, of which 13 were investigated for the first time and sampled on tropical coral reefs throughout the Indo-Pacific region. For newly sampled individuals, we sequenced the 16S rRNA, the nuclear locus comprising the complete ITS1-5.8S rRNA gene-ITS2 and the first intron of the calmodulin nuclear gene. Phylogenetic analyses of the data revealed and confirmed a general polyphyly, or doubtful monophyly, of all sampled genera in tropical regions based on both the mitochondrial and nuclear markers. Our results revealed that several morphological characters used today are unsuited to resolve phylogenetic relationships between species and genera, as well as the high phyletic diversity within this family. Future revision of the classification of this family will require extensive geographic sampling and the use of an integrative approach.
ISSN: 0300-3256

hal-01359414
https://hal.archives-ouvertes.fr/hal-01359414
DOI : 10.1111/zsc.12135

Éditeur(s) : HAL CCSD American Geophysical Union (AGU)
Résumé : International audience
This paper presents a new balanced structural cross-section of the Jaca thrust-sheet-top basin of the southern Pyrenees combined with paleo-thermometry and apatite fission track (AFT) thermochronology data. The cross-section, based on field data and interpretation of industrial seismic reflection profiles, allows refinement of previous interpretations of the south-directed thrust system, involving the identification of new thrust faults, and of the kinematic relationships between basement and cover thrusts from the middle Eocene to the early Miocene. AFT analysis shows a southward decrease in the level of fission track resetting, from totally reset Paleozoic rocks and lower Eocene turbidites (indicative of heating to Tmax > ~120 °C), to partially reset middle Eocene turbidites and no/very weak resetting in the upper Eocene-lower Oligocene molasse (Tmax < ~60 °C). AFT results indicate a late Oligocene-early Miocene cooling event throughout the Axial Zone and Jaca Basin. Paleo-maximum temperatures determined by vitrinite reflectance measurements and Raman spectroscopy of carbonaceous material reach up to ~240 °C at the base of the turbidite succession. Inverse modelling of AFT and vitrinite reflectance data with the QTQt software for key samples show compatibility between vitrinite-derived Tmax and the AFT reset level for most of the samples. However, they also suggest that the highest temperatures determined in the lowermost turbidites correspond to a thermal anomaly rather than burial heating, possibly due to fluid circulation during thrust activity. From these results, we propose a new sequential restoration of the south Pyrenean thrust system propagation and related basin evolution.
ISSN: 0278-7407

insu-01312746
https://hal-insu.archives-ouvertes.fr/insu-01312746
https://hal-insu.archives-ouvertes.fr/insu-01312746/document
https://hal-insu.archives-ouvertes.fr/insu-01312746/file/Labaume_et_al-2016-Tectonics.pdf
DOI : 10.1002/2016TC004192

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Ctenophores are a phylum of non-bilaterian marine (mostly planktonic) animals, characterised by several unique synapomorphies (e.g., comb rows, apical organ). Relationships between and within the nine recognised ctenophore orders are far from understood, notably due to a paucity of phylogenetically informative anatomical characters. Previous attempts to address ctenophore phylogeny using molecular data (18S rRNA) led to poorly resolved trees but demonstrated the paraphyly of the order Cydippida. Here we compiled an updated 18S rRNA data set, notably including a few newly sequenced species representing previously unsampled families (Lampeidae, Euryhamphaeidae), and we constructed an additional more rapidly evolving ITS1 + 5.8S rRNA + ITS2 alignment. These data sets were analysed separately and in combination under a probabilistic framework, using different methods (maximum likelihood, Bayesian inference) and models (e.g., doublet model to accommodate secondary structure; data partitioning). An important lesson from our exploration of these datasets is that the fast-evolving internal transcribed spacer (ITS) regions are useful markers for reconstructing high-level relationships within ctenophores. Our results confirm the paraphyly of the order Cydippida (and thus a ``cydippid-like'' ctenophore common ancestor) and suggest that the family Mertensiidae could be the sister group of all other ctenophores. The family Lampeidae (also part of the former ``Cydippida'') is probably the sister group of the order Platyctenida (benthic ctenophores). The order Beroida might not be monophyletic, due to the position of Beroe abyssicola outside of a clade grouping the other Beroe species and members of the ``Cydippida'' family Haeckeliidae. Many relationships (e.g. between Pleurobrachiidae, Beroida, Cestida, Lobata, Thalassocalycida) remain unresolved. Future progress in understanding ctenophore phylogeny will come from the use of additional rapidly evolving markers and improvement of taxonomic sampling.
ISSN: 0944-2006

hal-01544475
https://hal.archives-ouvertes.fr/hal-01544475
DOI : 10.1016/j.zool.2014.06.004

Résumé : Three species of man.-rove oysters, Crassostrea rhizophorae, C. brasiliana, and C. gasar, have been described along the Atlantic shores of South America and Africa. Because the distribution of these molluscs is of great biological and commercial interest, their taxonomy and distribution deserve further clarification. Therefore, 15 populations were sampled from both continents. Their 16S mitochondrial polymorphism was studied by sequencing and PCR-RFLP analysis. Two haplotypes were identified. Haplotype a was the only one observed in Africa, but it was also observed in South America together with haplotype b. Because C. gasar is the only mangrove oyster identified on the west coast of Africa, haplotype a was attributed to this species, which has thus been shown to occur in South America. Haplotype b is attributed to C. rhizophorae. The karyotypes of specimens of C. gasar, from Africa and from South America, were very similar, and both species were observed at the same location in Brazil. The occurrence of C. gasar in South America adds a third species-in addition to C rhizophorae and C. brasiliana-to the list of species present along these coasts. The predominant surface circulation patterns in this part of the Atlantic Ocean favor the hypothesis that C. gasar was transported from Africa to America. Finally, a phylogenetic tree built with seven 16S sequences from Crassostrea and Saccostrea species showed that C. gasar is intermediate between the American Crassostrea species (C virginica and C. rhizophorae) and the Asian species (C. gigas and C ariakensis).
Biological Bulletin (0006-3185), 2002-06 , Vol. 202 , N. 3 , P. 232-242

Droits : Marine Biological Laboratory.
http://archimer.ifremer.fr/doc/2002/publication-2790.pdf
http://archimer.ifremer.fr/doc/00000/2790/

Éditeur(s) : HAL CCSD BioMed Central
Résumé : [b]Background[/b][br/] [br/] The Amazonian rainforest is predicted to suffer from ongoing environmental changes. Despite the need to evaluate the impact of such changes on tree genetic diversity, we almost entirely lack genomic resources.[br/] [br/] [b]Results[/b][br/] [br/] In this study, we analysed the transcriptome of four tropical tree species (Carapa guianensis, Eperua falcata, Symphonia globulifera and Virola michelii) with contrasting ecological features, belonging to four widespread botanical families (respectively Meliaceae, Fabaceae, Clusiaceae and Myristicaceae). We sequenced cDNA libraries from three organs (leaves, stems, and roots) using 454 pyrosequencing. We have developed an R and bioperl-based bioinformatic procedure for de novo assembly, gene functional annotation and marker discovery. Mismatch identification takes into account single-base quality values as well as the likelihood of false variants as a function of contig depth and number of sequenced chromosomes. Between 17103 (for Symphonia globulifera) and 23390 (for Eperua falcata) contigs were assembled. Organs varied in the numbers of unigenes they apparently express, with higher number in roots. Patterns of gene expression were similar across species, with metabolism of aromatic compounds standing out as an overrepresented gene function. Transcripts corresponding to several gene functions were found to be over- or underrepresented in each organ. We identified between 4434 (for Symphonia globulifera) and 9076 (for Virola surinamensis) well-supported mismatches. The resulting overall mismatch density was comprised between 0.89 (S. globulifera) and 1.05 (V. surinamensis) mismatches/100 bp in variation-containing contigs.[br/] [br/] [b]Conclusion[/b][br/] [br/] The relative representation of gene functions in the four transcriptomes suggests that secondary metabolism may be particularly important in tropical trees. The differential representation of transcripts among tissues suggests differential gene expression, which opens the way to functional studies in these non-model, ecologically important species. We found substantial amounts of mismatches in the four species. These newly identified putative variants are a first step towards acquiring much needed genomic resources for tropical tree species.
ISSN: 1471-2164

hal-01032439
https://hal.archives-ouvertes.fr/hal-01032439
https://hal.archives-ouvertes.fr/hal-01032439/document
https://hal.archives-ouvertes.fr/hal-01032439/file/art_10-1186_1471-2164-15-238.pdf
DOI : 10.1186/1471-2164-15-238

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
In order to better constrain the relationship between tectonics and sedimentation of the Eastern Sardinian Margin, from the Messinian to the present day (METYSS project), a lithostratigraphic study was carried out on the Late Neogene deposits along the Cedrino Valley (eastern Sardinia). The late Neogene evolution is documented from sedimentological and tectonic analysis, biostratigraphic dating, and by mapping and logging stratigraphic sections. Previous authors have differentiated an early Pliocene marine formation from an older continental formation, possibly Miocene, the entire system being covered by late Pliocene to Quaternary lava flows. Preliminary biostratigraphic data suggest the absence of the lowermost Pliocene, based on the absence of Globorotalia margaritae and the presence of Globorotalia puncticulata, implying a sediment age between 3.81 and 2.41 Ma. At the foot of the Fiuli cliff, some mud clasts include a coccolith microflora, Tortonian in age, suggesting reworking. The Pliocene marine deposits consist of a single filling sequence instead of a succession of superimposed sequences as we would expect during this period of time; the occurrences of terms rarely respect the usual transgressive-regressive succession. Contrasting bathymetric environments (fore-shore, pro-delta, shelf or upper slope) can be abruptly superimposed on top of the other, along few meter thick intervals. A rapidly flooded term is observed in several sites and indicates a spatial variability over only a few kilometers distance. Some deep water deposits are in the middle of the infilling Pliocene sequence, whereas shallower water deposits can be repeated along a vertical section, or even interrupted by emersion. These marked differences can express syn-, or possibly post-sedimentation tectonic uplifts. The 10–25° bed dips originated through local tectonic uplift. At Fiuli, the geometry of the bedding planes is indicative of tilting toward the west, in a direction opposite to the one observed at Onifai. These Pliocene series form a wide syncline with an approximately NNE–SSW axis. This morpho-structural behavior appears to be largely atypical of this East-Sardinian coastal area.
ISSN: 1040-6182

hal-01134707
https://hal.archives-ouvertes.fr/hal-01134707
DOI : 10.1016/j.quaint.2014.11.022

Éditeur(s) : HAL CCSD
Résumé : International audience
Given a topological R-module or algebra E and an asymptotic scale MR Λ, we define a natural M-extended topology on the sequence space E Λ, and the M-extension of E as the Hausdorff space associated with the subspace of sequences for which multiplication is continuous with respect to this topology. Colombeau's generalized functions and similar constructions are obtained as special cases, but this new approach also allows the iteration of the construction, which was not possible with previously existing theories. We use only the topology, i.e. neigbourhoods of zero, but not its explicit definition in terms of seminorms, inductive or projective limits etc., which is particularly useful in non-metrizable spaces. Many ideas commonly used in generalized function spaces (functoriality, association, sheaf structure, algebraic analysis, ...) can be applied to a large extent; but reasoning on a category-theoretic level allows the establishment of several results so far only known for particular cases, to the whole class of such spaces.
Integral Transforms and Special Functions
Bedlewo, Poland

hal-00761666
https://hal.univ-antilles.fr/hal-00761666
DOI : 10.1080/10652460802565040

Éditeur(s) : HAL CCSD SPRINGER
Résumé : International audience
A key question in evolutionary biology is the reproducibility of adaptation. This question can now be quantitatively analyzed using experimental evolution coupled to whole genome sequencing (WGS). With complete sequence data, one can assess convergence among replicate populations. In turn, convergence reflects the action of natural selection and also the breadth of the field of possible adaptive solutions. That is, it provides insight into how many genetic solutions or adaptive paths may lead to adaptation in a given environment. Convergence is both a property of an adaptive landscape and, reciprocally, a tool to study that landscape. In this chapter we present the links between convergence and the properties of adaptive landscapes with respect to two types of microbial experimental evolution. The first tries to reconstruct a full adaptive landscape using a handful of carefully identified mutations (the reductionist approach), while the second uses WGS of replicate experiments to infer properties of the adaptive landscape. Reductionist approaches have highlighted the importance of epistasis in shaping the adaptive landscape, but have also uncovered a wide diversity of landscape architectures. The WGS approach has uncovered a very high diversity of beneficial mutations that affect a limited set of genes or functions and also suggests some shortcomings of the reductionist approach. We conclude that convergence may be better defined at an integrated level, such as the genic level or even at a phenotypic level, and that integrated mechanistic models derived from systems biology may offer an interesting perspective for the analysis of convergence at all levels.
ECOLOGICAL GENOMICS: ECOLOGY AND THE EVOLUTION OF GENES AND GENOMES

ISBN : 978-94-007-7347-9; 978-94-007-7346-2
hal-01544757
https://hal.archives-ouvertes.fr/hal-01544757
DOI : 10.1007/978-94-007-7347-9__11

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
3D seismic data located in the Gjallar Ridge (Vøring Basin, offshore Norway) reveals a closely-spaced polygonal fault system affecting more than 800 m of homogeneous mud-dominated Quaternary and Tertiary sequences. As some faults reach the modern seafloor, they represent an active polygonal fault system at present day. Even if the processes remain unclear and are still under debate, it is generally agreed that the initiation of polygonal faults is the result of shallow burial dewatering of fine-grained unconsolidated sediments by volumetric compaction. 3D seismic data are commonly interpreted by propagating horizons automatically and by picking faults manually. However, in the case of polygonal fault intervals, this approach is time consuming due to the huge number of faults and because automatic propagation can be misleading. In this study, we applied a new technique of 3D seismic interpretation based on a sequential stratigraphy analysis, using the new PaleoScan© software (Eliis Company). It allowed us to build a 3D geological model computing more than 300 horizons within the faulted intervals. We then used the coherency attribute, depicting anomalies in the shape of seismic waveform like faults, in order to constrain a possible link between fault distribution and stratigraphic levels. Our approach allows fault throws to be calculated in milliseconds on any polygonal fault plane. The result shows that fault segments have been reactivated by dip-linkage. Distribution of faults depends on mechanical units, intervals characterized by different petrophysical properties, which are independent from lithological and diagenetic changes. According to these results, we propose a model showing the evolution of polygonal fault intervals in which faulting stages are separated by a quiescence phase during burial. A first tier of polygonal faults is initiated at a specific depth, according to the Cam-clay model. Then, following a period of quiescence during which mud-rich sediments continued to accumulate, new fault segments are initiated above the first mechanical unit and within this undeformed interval. New nucleated faults then connect downward to pre-existing underlying polygonal fault system, thus progressively increasing the thickness of the faulted interval.
ISSN: 0025-3227

hal-00772470
https://hal.archives-ouvertes.fr/hal-00772470
DOI : 10.1016/j.margeo.2012.07.016

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Background: The filamentous fungus Trichoderma reesei is the main industrial cellulolytic enzyme producer. Several strains have been developed in the past using random mutagenesis, and despite impressive performance enhancements, the pressure for low-cost cellulases has stimulated continuous research in the field. In this context, comparative study of the lower and higher producer strains obtained through random mutagenesis using systems biology tools (genome and transcriptome sequencing) can shed light on the mechanisms of cellulase production and help identify genes linked to performance. Previously, our group published comparative genome sequencing of the lower and higher producer strains NG 14 and RUT C30. In this follow-up work, we examine how these mutations affect phenotype as regards the transcriptome and cultivation behaviour. Results: We performed kinetic transcriptome analysis of the NG 14 and RUT C30 strains of early enzyme production induced by lactose using bioreactor cultivations close to an industrial cultivation regime. RUT C30 exhibited both earlier onset of protein production (3 h) and higher steady-state productivity. A rather small number of genes compared to previous studies were regulated (568), most of them being specific to the NG 14 strain (319). Clustering analysis highlighted similar behaviour for some functional categories and allowed us to distinguish between induction-related genes and productivity-related genes. Cross-comparison of our transcriptome data with previously identified mutations revealed that most genes from our dataset have not been mutated. Interestingly, the few mutated genes belong to the same clusters, suggesting that these clusters contain genes playing a role in strain performance. Conclusions: This is the first kinetic analysis of a transcriptomic study carried out under conditions approaching industrial ones with two related strains of T. reesei showing distinctive cultivation behaviour. Our study sheds some light on some of the events occurring in these strains following induction by lactose. The fact that few regulated genes have been affected by mutagenesis suggests that the induction mechanism is essentially intact compared to that for the wild-type isolate QM6a and might be engineered for further improvement of T. reesei. Genes from two specific clusters might be potential targets for such genetic engineering.
ISSN: 1754-6834

Droits : http://creativecommons.org/licenses/by/
hal-01112360
http://hal.upmc.fr/hal-01112360
http://hal.upmc.fr/hal-01112360/document
http://hal.upmc.fr/hal-01112360/file/Poggi-Parodi_2014_Kinetic.pdf
DOI : 10.1186/s13068-014-0173-z

Éditeur(s) : HAL CCSD Taylor & Francis
Résumé : International audience
We review our recent formulation of Colombeau-type algebras as Hausdorff sequence spaces with ultranorms, defined by sequences of exponential weights. We extend previous results and give new perspectives related to echelon-type spaces, possible generalizations, asymptotic algebras, concepts of association, and applications thereof.
ISSN: 1065-2469

hal-00758570
https://hal.univ-antilles.fr/hal-00758570
https://hal.univ-antilles.fr/hal-00758570/document
https://hal.univ-antilles.fr/hal-00758570/file/0705.2739v1.pdf
DOI : 10.1080/10652460500437807

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
Tuftelin (TUFT1) is an acidic, phosphorylated glycoprotein, initially discovered in developing enamel matrix. TUFT1 is expressed in many mineralized and non-mineralized tissues. We performed an evolutionary analysis of 82 mammalian TUFT1 sequences to identify residues and motifs that were conserved during 220 million years (Ma) of evolution. We showed that 168 residues (out of the 390 residues composing the human TUFT1 sequence) are under purifying selection. Our analyses identified several, new, putatively functional domains and confirmed previously described functional domains, such as the TIP39 interaction domain, which correlates with nuclear localization of the TUFT1 protein, that was demonstrated in several tissues. We also identified several sites under positive selection, which could indicate evolutionary changes possibly related to the functional diversification of TUFT1 during evolution in some lineages. We discovered that TUFT1 and MYZAP (myocardial zonula adherens protein) share a common ancestor that was duplicated circa 500 million years ago. Taken together, these findings expand our knowledge of TUFT1 evolution and provide new information that will be useful for further investigation of TUFT1 functions.
ISSN: 0022-2844

hal-01516886
http://hal.upmc.fr/hal-01516886
http://hal.upmc.fr/hal-01516886/document
http://hal.upmc.fr/hal-01516886/file/Delgado_2017_Evolutionary.pdf
DOI : 10.1007/s00239-017-9789-5

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Background: The relative scarcity of Copia retrotransposons has been recently characterized in metazoans in comparison with the other superfamilies of LTR elements. Furthermore, Copia retrotransposons have often a particular dynamics that results in a highly predominant single clade of elements within a large host taxon, such as the GalEa-like retrotransposons in crustaceans. Taking advantage of the skyrocketing amount of genomic data available for fungi, we carried out the first large-scale comparative genomic analysis of the Copia clades in filamentous ascomycetes.Results: Screening 30 completely sequenced genomes allowed us to identify more than 2500 Copia copies with conserved LTR, which are distributed in 138 families. Their characterization revealed that fungal Copia diversity is much broader than previously thought with at least 27 clades, 23 of which likely correspond to new ones. While the Copia copy number is low in most species, the two clades GalEa and FunCo1 are widely distributed and highly dominate Copia content as they both account for 80% of the detected sequences.Conclusions: In Fungi, GalEa retrotransposons are restricted to Pezizomycotina in which they can make up an outstandingly high proportion of the genome (up to 10% in Cenococcum geophilum). At last, we revealed that fungal GalEa elements structurally differ from all other Copia elements with an absence of Primer Binding Site. These elements however harbor a Conserved Hairpin Site which is probably essential for their transposition.sequences.
ISSN: 1471-2164

Droits : http://creativecommons.org/licenses/by/
hal-01529914
http://hal.upmc.fr/hal-01529914
http://hal.upmc.fr/hal-01529914/document
http://hal.upmc.fr/hal-01529914/file/art_10.1186_s12864-017-3795-2.pdf
DOI : 10.1186/s12864-017-3795-2

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Background: The Ras/Raf/MEK/ERK signaling pathway is involved in essential cell processes and it is abnormally activated in similar to 30 % of cancers and cognitive disorders. Two ERK isoforms have been described, ERK1 and ERK2; ERK2 being regarded by many as essential due to the embryonic lethality of ERK2 knock-out mice, whereas mice lacking ERK1 are viable and fertile. The controversial question of why we have two ERKs and whether they have differential functions or display functional redundancy has not yet been resolved. Results: To investigate this question we used a novel approach based on comparing the evolution of ERK isoforms' sequences and protein expression across vertebrates. We gathered and cloned erk1 and erk2 coding sequences and we examined protein expression of isoforms in brain extracts in all major clades of vertebrate evolution. For the first time, we measured each isoforms' relative protein level in phylogenetically distant animals using anti-phospho antibodies targeting active ERKs. We demonstrate that squamates (lizards, snakes and geckos), despite having both genes, do not express ERK2 protein whereas other tetrapods either do not express ERK1 protein or have lost the erk1 gene. To demonstrate the unexpected squamates' lack of ERK2 expression, we targeted each ERK isoform in lizard primary fibroblasts by specific siRNA-mediated knockdown. We also found that undetectable expression of ERK2 in lizard is compensated by a greater strength of lizard's erk1 promoter. Finally, phylogenetic analysis revealed that ERK1 amino acids sequences evolve faster than ERK2' s likely due to genomic factors, including a large difference in gene size, rather than from functional differences since amino acids essential for function are kept invariant. Conclusions: ERK isoforms appeared by a single gene duplication at the onset of vertebrate evolution at least 400 Mya. Our results demonstrate that tetrapods can live by expressing either one or both ERK isoforms, supporting the notion that ERK1/2 act interchangeably. Substrate recognition sites and catalytic cleft are nearly invariant in all vertebrate ERKs further suggesting functional redundancy. We suggest that future ERK research should shift towards understanding the role and regulation of total ERK quantity, especially in light of newly described erk2 gene amplification identified in tumors.
ISSN: 1471-2148

hal-01546165
https://hal.archives-ouvertes.fr/hal-01546165
DOI : 10.1186/s12862-015-0450-x

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
Marine protist diversity inventories have largely focused on planktonic environments, while benthic protists have received relatively little attention. We therefore hypothesize that current diversity surveys have only skimmed the surface of protist diversity in marine sediments, which may harbor greater diversity than planktonic environments. We tested this by analyzing sequences of the hypervariable V4 18S rRNA from benthic and planktonic protist communities sampled in European coastal regions. Despite a similar number of OTUs in both realms, richness estimations indicated that we recovered at least 70% of the diversity in planktonic protist communities, but only 33% in benthic communities. There was also little overlap of OTUs between planktonic and benthic communities, as well as between separate benthic communities. We argue that these patterns reflect the heterogeneity and diversity of benthic habitats. A comparison of all OTUs against the Protist Ribosomal Reference database showed that a higher proportion of benthic than planktonic protist diversity is missing from public databases; similar results were obtained by comparing all OTUs against environmental references from NCBI's Short Read Archive. We suggest that the benthic realm may therefore be the world's largest reservoir of marine protist diversity, with most taxa at present undescribed.
ISSN: 0168-6496

hal-01383722
http://hal.upmc.fr/hal-01383722
http://hal.upmc.fr/hal-01383722/document
http://hal.upmc.fr/hal-01383722/file/Forster_2016_Benthic_protists.pdf
DOI : 10.1093/femsec/fiw120

Éditeur(s) : HAL CCSD Microbiology Society
Résumé : International audience
An actinobacterial strain, designated ViU22(T), was isolated from a natural uranium-rich soil and was studied using a polyphasic approach. Cells formed orange-pigmented colonies, were rod-shaped, Gram-positive (non-staining method), non-motile and non-spore-forming. This organism grew in 0-4.5 % (w/v) NaCl and at 15-37 °C, with optimal growth occurring in 0.5 % (w/v) NaCl and at 30 °C. Comparative 16S rRNA gene sequence analysis revealed that the strain ViU22(T) belonged to the genus Microbacterium. It exhibited highest 16S rRNA gene sequence similarity with the type strains of Microbacterium testaceum (98.14 %) and Microbacterium binotii (98.02 %). The DNA-DNA relatedness of strains ViU22(T) with the most closely related type strains Microbacterium testaceum and Microbacterium binotii DSM 19164(T) was 20.10 % (± 0.70) and 28.05 % (± 0.35), respectively. Strain ViU22(T) possessed a type B2β peptidoglycan with partial substitution of glutamic acid by 3-hydroxy glutamic acid. The major menaquinones were MK-11 and MK-12. Major polar lipids detected in the strain ViU22(T) were diphosphatidylglycerol, phosphatidylglycerol, an unknown phospholipid and unknown glycolipids. The predominant fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0, a pattern reported for other Microbacterium species. The major cell-wall sugars were galactose, xylose and mannose and the DNA G+C content was 71 mol%. Together, the DNA-DNA hybridization results and the differentiating phenotypic characteristics, showed that strain ViU22(T) should be classified as the type strain of a novel species within the genus Microbacterium, for which the name Microbacterium lemovicicum sp. nov. is proposed. The type strain is ViU22(T) ( = ATCC BAA-2396(T) = CCUG 62198(T) = DSM 25044(T)).
ISSN: 1466-5026

hal-01561095
https://hal-amu.archives-ouvertes.fr/hal-01561095
PUBMED : 23264499
DOI : 10.1099/ijs.0.048454-0

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699
Spontaneous gene flow between wild and cultivated chicory, Cichorium intybus L., may have implications for the genetic structure and evolution of populations and varieties. One aspect of this crop-wild gene flow is the dispersal of transgenes from genetically modified varieties, e.g. gene flow from GM chicory to natural chicory could have unwanted consequences. With the purpose to identify and quantify crop-wild gene flow in chicory, we analysed introgression in 19 wild chicory populations and 16 accessions of chicory varieties and landraces distributed across Northern, Central and Mediterranean Europe. The analysis used 281 AFLP markers and 75 SSAP markers giving a total of 356 polymorphic markers. Results from model based assignments with the program STRUCTURE indicated many incidents of recent gene flow. Gene flow was observed both between cultivars and wild populations, between landraces and wild populations, between different wild populations as well as between cultivars. Population structure visualized by distance-based clustering showed a North-South geographical structuring of the wild populations, and a general grouping of the cultivars corresponding to known origin. The results indicated, however, that the structuring between the two groups of wild and cultivated types was weak. As crop and wild recipients are genetically close and genes are transferred between the two types rather frequently, focus on mitigating crop-wild gene flow should be increased, before transgenic varieties are cultivated openly.
ISSN: 0925-9864

hal-01032184
https://hal.archives-ouvertes.fr/hal-01032184
DOI : 10.1007/s10722-008-9375-1

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Anisotropy of low-field magnetic susceptibility (AMS) of basaltic lava flows can give some clues about post-emplacement tilting occurring in volcanic sequences. Such a study has been carried out on a sequence of 19 successive lava flows from Kerguelen Archipelago. Surprisingly, two different patterns were observed. The first one - herein called normal fabric - is consistent with the lava-flow direction inferred from geological observations, whereas the second one observed for about 70 per cent of the analysed samples - herein called abnormal fabric - appears to be unrelated to the shear history of the lava flows during their emplacements. These abnormal fabrics are not strictly inverse fabric but seem to have a more complex origin. The unusual nature of these abnormal fabrics has been confirmed by lattice preferred orientation of plagioclases obtained from high-resolution electron backscattered diffraction measurements. The aim of this study is to propose a physical interpretation of these fabrics. A first step in our understanding was to clearly identify the nature and the magnetic properties of the Fe-Ti oxides assemblage. Thus, we present a comprehensive rock magnetic analysis relying on low- and high-temperature thermomagnetic curves (K-T), crossover diagrams, first-order reversal curves, ore-microscopy, Mössbauer measurements and electron backscattered images. We found that in the present case the abnormal fabrics are probably linked to a mixture of prevailing single domain (SD) strongly interacting grains population and a subsidiary multidomain grains population. SD grains are identified as small magnetite crystallized within the interstitial glass in globular aggregates along the silicate framework. Then a question arises: to what extent such SD interacting grains in globular aggregates can affect the magnetic susceptibility and its anisotropy? To answer this question, we developed a physical model in which the total energy density of an SD grain with an uniaxial anisotropy is minimized. In this model, the distribution function of the direction of the magnetic interaction field is comprised between two boundary states. It is either isotropic, which formally corresponds to the thermal demagnetized state, or it is ordered, which formally corresponds to the Alternative Field demagnetized state. We show that in both cases the degree of anisotropy decreases as the interaction field increases. Thus, we conclude that the abnormal fabric encountered in this study can be simply explained by strong magnetostatic interactions that would explain the large scattering of AMS often observed in basaltic lava flows.
ISSN: 0956-540X

hal-00716449
https://hal.archives-ouvertes.fr/hal-00716449
https://hal.archives-ouvertes.fr/hal-00716449/document
https://hal.archives-ouvertes.fr/hal-00716449/file/gji-S-12-HAL.pdf
DOI : 10.1111/J.1365-246X.2012.05421.X

Éditeur(s) : HAL CCSD Society for Molecular Biology and Evolution
Résumé : International audience
Although heterokaryons have been reported in nature, multicellular organisms are generally assumed genetically homogeneous. Here, we investigate the case of arbuscular mycorrhizal fungi (AMF) that form symbiosis with plant roots. The growth advantages they confer to their hosts are of great potential benefit to sustainable agricultural practices. However, measuring genetic diversity for these coenocytes is a major challenge: Within the same cytoplasm, AMF contain thousands of nuclei and show extremely high levels of genetic variation for some loci. The extent and physical location of polymorphism within and between AMF genomes is unclear. We used two complementary strategies to estimate genetic diversity in AMF, investigating polymorphism both on a genome scale and in putative single copy loci. First, we used data from whole-genome pyrosequencing of four AMF isolates to describe genetic diversity, based on a conservative network-based clustering approach. AMF isolates showed marked differences in genome-wide diversity patterns in comparison to a panel of control fungal genomes. This clustering approach further allowed us to provide conservative estimates of Rhizophagus spp. genomes sizes. Second, we designed new putative single copy genomic markers, which we investigated by massive parallel amplicon sequencing for two Rhizophagus irregularis and one Rhizophagus sp. isolates. Most loci showed high polymorphism, with up to 103 alleles per marker. This polymorphism could be distributed within or between nuclei. However, we argue that the Rhizophagus isolates under study might be heterokaryotic, at least for the putative single copy markers we studied. Considering that genetic information is the main resource for identification of AMF, we suggest that special attention is warranted for the study of these ecologically important organisms.
ISSN: 1759-6653

Droits : http://creativecommons.org/licenses/by/
hal-01224215
http://hal.upmc.fr/hal-01224215
http://hal.upmc.fr/hal-01224215/document
http://hal.upmc.fr/hal-01224215/file/Genome%20Biol%20Evol-2015-Boon-505-21.pdf
DOI : 10.1093/gbe/evv002