Inversing the natural hydrogen bonding rule to selectively amplify GC-rich ADAR-edited RNAs

DNA complementarity is expressed by way of three hydrogen bonds for a G:C base pair and two for A:T. As a result, careful control of the denaturation temperature of PCR allows selective amplification of AT-rich alleles. Yet for the same reason, the converse is not possible, selective amplification of GC-rich alleles. Inosine (I) hydrogen bonds to cytosine by two hydrogen bonds while diaminopurine (D) forms three hydrogen bonds with thymine. By substituting dATP by dDTP and dGTP by dITP in a PCR reaction, DNA is obtained in which the natural hydrogen bonding rule is inversed. When PCR is performed at limiting denaturation temperatures, it is possible to recover GC-rich viral genomes and inverted Alu elements embedded in cellular mRNAs resulting from editing by dsRNA dependent host cell adenosine deaminases. The editing of Alu elements in cellular mRNAs was strongly enhanced by type I interferon induction indicating a novel link mRNA metabolism and innate immunity.     

Ezrin/Radixin/Moesin Are Required for the Purinergic P2X7 Receptor (P2X7R)-dependent Processing of the Amyloid Precursor Protein

The amyloid precursor protein (APP) can be cleaved by α-secretases in neural cells to produce the soluble APP ectodomain (sAPPα), which is neuroprotective. We have shown previously that activation of the purinergic P2X7 receptor (P2X7R) triggers sAPPα shedding from neural cells. Here, we demonstrate that the activation of ezrin, radixin, and moesin (ERM) proteins is required for the P2X7R-dependent proteolytic processing of APP leading to sAPPα release. Indeed, the down-regulation of ERM by siRNA blocked the P2X7R-dependent shedding of sAPPα. We also show that P2X7R stimulation triggered the phosphorylation of ERM. Thus, ezrin translocates to the plasma membrane to interact with P2X7R. Using specific pharmacological inhibitors, we established the order in which several enzymes trigger the P2X7R-dependent release of sAPPα. Thus, a Rho kinase and the MAPK modules ERK1/2 and JNK act upstream of ERM, whereas a PI3K activity is triggered downstream. For the first time, this work identifies ERM as major partners in the regulated non-amyloidogenic processing of APP.     

Controlling IL-7 Injections in HIV-Infected Patients

Immune interventions consisting in repeated injections are broadly used as they are thought to improve the quantity and the quality of the immune response. However, they also raise several questions that remain unanswered, in particular the number of injections to make or the delay to respect between different injections to achieve this goal. Practical and financial considerations add constraints to these questions, especially in the framework of human studies. We specifically focus here on the use of interleukin-7 (IL-7) injections in HIV-infected patients under antiretroviral treatment, but still unable to restore normal levels of \(\hbox {CD}4^{+}\) T lymphocytes. Clinical trials have already shown that repeated cycles of injections of IL-7 could help maintaining \(\hbox {CD}4^{+}\) T lymphocytes levels over the limit of 500 cells/\(\upmu \)L, by affecting proliferation and survival of \(\hbox {CD}4^{+}\) T cells. We then aim at answering the question: how to maintain a patients level of \(\hbox {CD}4^{+}\) T lymphocytes by using a minimum number of injections (i.e., optimizing the strategy of injections)? Based on mechanistic models that were previously developed for the dynamics of \(\hbox {CD}4^{+}\) T lymphocytes in this context, we model the process by a piecewise deterministic Markov model. We then address the question by using some recently established theory on impulse control problem in order to develop a numerical tool determining the optimal strategy. Results are obtained on a reduced model, as a proof of concept: the method allows to define an optimal strategy for a given patient. This method could be applied to optimize injections schedules in clinical trials.     

Characterization of Six Leuconostoc fallax Bacteriophages Isolated from an Industrial Sauerkraut Fermentation

Six bacteriophages active against Leuconostoc fallax strains were isolated from industrial sauerkraut fermentation brines. These phages were characterized as to host range, morphology, structural proteins, and genome fingerprint. They were exclusively lytic against the species L. fallax and had different host ranges among the strains of this species tested. Morphologically, three of the phages were assigned to the family Siphoviridae, and the three others were assigned to the family Myoviridae. Major capsid proteins detected by electrophoresis were distinct for each of the two morphotypes. Restriction fragment length polymorphism analysis and randomly amplified polymorphic DNA fingerprinting showed that all six phages were genetically distinct. These results revealed for the first time the existence of bacteriophages that are active against L. fallax and confirmed the presence and diversity of bacteriophages in a sauerkraut fermentation. Since a variety of L. fallax strains have been shown to be present in sauerkraut fermentation, bacteriophages active against L. fallax are likely to contribute to the microbial ecology of sauerkraut fermentation and could be responsible for some of the variability observed in this type of fermentation.     

Taxonomic review of the “Bulimes”, terrestrial gastropods from the continental Eocene of the Hamada de Méridja (northwestern Sahara,Algeria) (Mollusca: Stylommatophora: Strophocheilidae?), with a discussion of the genera of the family Vidaliellidae

Terrestrial gastropods occur in many North African localities in Eocene continental deposits. Here we analyse the faunal assemblage from the Hamada de Méridja Formation in southwestern Algeria, dated as Early to Middle Eocene on the basis of charophytes. The assemblage consists of three closely related species that to date have been classified either in the extant Madagascan genus Leucotaenius v. Martens, 1860, or in the SW European Eocene genera Romanella Jodot, 1957 and Vicentinia Jodot, 1957. This is rejected for shell morphological and phylogeographical reasons, and a new classification as Maghrebiola gen. nov. is proposed. Maghrebiola is tentatively placed in the South American family Strophocheilidae, as species from the Early Eocene Itaboraí Basin of Brazil, currently placed in the genus Eoborus Klappenbach and Olazarri, 1970 in the family Strophocheilidae, superfamily Acavoidea, have a very similar shell habitus. This record possibly extends the known geographical range of the Strophocheilidae into the African continent during the Eocene. Immigration of this stock into North Africa during the Cretaceous via a still existing plate connection is assumed. An attribution of Maghrebiola to the African family Achatinidae is unlikely for shell morphological reasons despite certain habitus similarities, although the Priabonian genera Arabicolaria and Pacaudiella from Oman most likely belong into this family, and not to the Vidaliellidae as originally proposed. Possible causes for the very low diversity of the assemblage are mainly unfavourable living conditions, i.e. a relatively dry climate resulting in sparse vegetation and only occasional presence of water bodies, which may have had increased salinities, accounting for the lack of freshwater mollusks. The absence of any competing large gastropods may possibly have facilitated high intraspecific variability leading to sympatric occurrence of three closely related species, due to the animals occupying a wide range of available ecological niches. As the species discussed here have also been attributed to the genera Romanella and Vicentinia in the Vidaliellidae, we provide an appendix with annotated characterisations of most genera of the Vidaliellidae and list the nominal species assigned to them. This family is tentatively placed in the South American superfamily Orthalicoidea; its stock would have similarly immigrated from South America, but have successfully colonized mainly SW Europe, with only one Eocene species [Romanella kantarensis (Jodot, 1936)] recognized in Algeria.     

Occurrence of Listeria spp. in Effluents of French Urban Wastewater Treatment Plants

Listeria spp. were found in most treated waters (84.4%) and raw sludge (89.2%) of six French urban wastewater treatment plants and one composting facility, examined monthly over a 1-year period. Most strains belonged to Listeria monocytogenes, serotypes 4b/4e being predominant. Sludge composting and liming reduced or prevented Listeria contamination.     

Variabilité dentaire et crânienne de Numidotherium koholense (Mammalia, Proboscidea) de l’Éocène d’El Kohol, Algérie

The variability of one of the oldest known proboscideans, Numidotherium koholense from the Lower Eocene of El Kohol, Algeria, is here examined. The biometrical study of the jugal teeth shows that the population is homogeneous and corresponds to a single species. The important variations of the skull's shape are interpreted as resulting from sexual dimorphism. The dental variability is analysed and discussed from an evolutionary perspective regarding the adaptative radiation of the proboscidean order at the beginning of the Tertiary.     

Slow relaxation of the magnetization in high-nuclearity Ln-complexes

By the surface modification strategy, a novel high-nuclearity lanthanide complex with a discrete structure, Er₂₆I(μ₃-OH)₂₀(μ₃-O)₆(NO₃)₉(IN)₃₃(OH)₃(H₂O)₃₃ (noted Er₂₆, HIN = isonicotinic acid), has been prepared under hydrothermal conditions. The magnetic properties of Er₂₆ and two analogue dysprosium assemblies Dy₃₀I(μ₃-OH)₂₄(μ₃-O)₆(NO₃)₉(IN)₄₁(OH)₃(H₂O)₃₈ (noted Dy₂₆-I) and Dy₂₆I(μ₃-OH)₂₀(μ₃-O)₆(NO₃)₉(IN)_31.25(OH)_4.75(H₂O)_41.75 (noted Dy₂₆-II) have been studied. The results show that the slow relaxation of the magnetization is newly found in Dy₂₆-I constructed from {Dy₂₆} and {Dy₄} cluster units. The {Dy₄} units in Dy₂₆-I, the relative orientation of the complex or the inter-molecular interactions between {Dy₂₆} cores might play an important role in the origin of this magnetic behavior.     

Phage response to CRISPR-encoded resistance in Streptococcus thermophilus

Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated genes are linked to a mechanism of acquired resistance against bacteriophages. Bacteria can integrate short stretches of phage-derived sequences (spacers) within CRISPR loci to become phage resistant. In this study, we further characterized the efficiency of CRISPR1 as a phage resistance mechanism in Streptococcus thermophilus. First, we show that CRISPR1 is distinct from previously known phage defense systems and is effective against the two main groups of S. thermophilus phages. Analyses of 30 bacteriophage-insensitive mutants of S. thermophilus indicate that the addition of one new spacer in CRISPR1 is the most frequent outcome of a phage challenge and that the iterative addition of spacers increases the overall phage resistance of the host. The added new spacers have a size of between 29 to 31 nucleotides, with 30 being by far the most frequent. Comparative analysis of 39 newly acquired spacers with the complete genomic sequences of the wild-type phages 2972, 858, and DT1 demonstrated that the newly added spacer must be identical to a region (named proto-spacer) in the phage genome to confer a phage resistance phenotype. Moreover, we found a CRISPR1-specific sequence (NNAGAAW) located downstream of the proto-spacer region that is important for the phage resistance phenotype. Finally, we show through the analyses of 20 mutant phages that virulent phages are rapidly evolving through single nucleotide mutations as well as deletions, in response to CRISPR1.