Versatile gene-specific sequence tags for Arabidopsis functional genomics: transcript profiling and reverse genetics applications.

Microarray transcript profiling and RNA interference are two new technologies crucial for large-scale gene function studies in multicellular eukaryotes. Both rely on sequence-specific hybridization between complementary nucleic acid strands, inciting us to create a collection of gene-specific sequence tags (GSTs) representing at least 21,500 Arabidopsis genes and which are compatible with both approaches. The GSTs were carefully selected to ensure that each of them shared no significant similarity with any other region in the Arabidopsis genome. They were synthesized by PCR amplification from genomic DNA. Spotted microarrays fabricated from the GSTs show good dynamic range, specificity, and sensitivity in transcript profiling experiments. The GSTs have also been transferred to bacterial plasmid vectors via recombinational cloning protocols. These cloned GSTs constitute the ideal starting point for a variety of functional approaches, including reverse genetics. We have subcloned GSTs on a large scale into vectors designed for gene silencing in plant cells. We show that in planta expression of GST hairpin RNA results in the expected phenotypes in silenced Arabidopsis lines. These versatile GST resources provide novel and powerful tools for functional genomics.

La mémoire et le temps. Mélanges offerts à Pierre Bonnard

Vingt-et-un biblistes de Suisse, de France, d'Allemagne et d'Italie se rassemblent autour d'un thème qui n'est pas seule­ment très actuel. Ce thème a été aperçu par Pierre Bonnard comme une structure fondamentale dans la théologie du Nou­veau Testament: le souvenir, l'anamnèse. Faire mémoire de Jésus pour comprendre le temps présent. La mémoire du Jésus terrestre est cette structure qui gouverne la vie et la pensée des premiers chrétiens ; elle est le lieu des combats théologiques de Paul, de Luc, de Matthieu, de Jean... Lieu de toutes les fidélités et de toutes les déviances. Vingt-et-un exégètes reprennent ce thème, pour en mesurer la fécondité dans le champ textuel qui leur est familier. Quel rôle joue au premier siècle la mémoire de l'histoire originaire, au gré du temps qui passe? Comment décrire, et apprécier théologiquement, la relecture de l'histoire de Jésus à laquelle procèdent les auteurs du Nouveau Testament? Ces contri­butions sont un hommage à Pierre Bonnard et à son oeuvre d'exégète du Nouveau Testament.

Jésus et la Loi dans la mémoire des premiers chrétiens

(Résumé de l'ouvrage) Vingt-et-un biblistes de Suisse, de France, d'Allemagne et d'Italie se rassemblent autour d'un thème qui n'est pas seule­ment très actuel. Ce thème a été aperçu par Pierre Bonnard comme une structure fondamentale dans la théologie du Nou­veau Testament: le souvenir, l'anamnèse. Faire mémoire de Jésus pour comprendre le temps présent. La mémoire du Jésus terrestre est cette structure qui gouverne la vie et la pensée des premiers chrétiens ; elle est le lieu des combats théologiques de Paul, de Luc, de Matthieu, de Jean... Lieu de toutes les fidélités et de toutes les déviances. Vingt-et-un exégètes reprennent ce thème, pour en mesurer la fécondité dans le champ textuel qui leur est familier. Quel rôle joue au premier siècle la mémoire de l'histoire originaire, au gré du temps qui passe? Comment décrire, et apprécier théologiquement, la relecture de l'histoire de Jésus à laquelle procèdent les auteurs du Nouveau Testament? Ces contri­butions sont un hommage à Pierre Bonnard et à son oeuvre d'exégète du Nouveau Testament.

Pre- and post-treatment immunodiagnostic evaluation in human schistosomiasis mansoni

Schistosomiasis control seems to be different in countries were low parasitic burden and asymptomatic clinical patients are the features of majority of cases. Immunological methods must substitute the traditional coprologic techniques used for some decades in the Control Program. Circumoval Precipitin Test (COPT), intradermal test and ELISA with soluble egg antigen (SEA) are evaluated for using as tools for seroepidemiologic studies. COPT and ELISA were performed after treatment to known their utility when impact of chemotherapy must be assessed. One hundred sixty five persons were followed up 3, 6, 9 and 12 months after treatment. The mean sensitivity of CPT studied by age groups was 95.6% which is very important considering that 88.4% of the studied population excreted less than 100 egg/gr of feces, while sensitivity of intradermal test was 58.2%. Children showed the highest ractivity to COPT. When treatment is effective, COPT reactivity progressively disminish until become negative one year later. In the non cure group, the COPT reactivity disminished but never below 20%. ELISA-SEA did not modify one year after treatment. Effort should be made to isolate fractions of eggs Schistosoma mansoni whose antibodies disappear after treatment.

Protective effects of hypercapnic acidosis on ventilator-induced lung injury.

To investigate whether respiratory acidosis modulates ventilator-induced lung injury (VILI), we perfused (constant flow) 21 isolated sets of normal rabbit lungs, ventilated them for 20 min (pressure controlled ventilation [PCV] = 15 cm H(2)O) (Baseline) with an inspired CO(2) fraction adjusted for the partial pressure of CO(2) in the perfusate (PCO(2) approximately equal to 40 mm Hg), and then randomized them into three groups. Group A (control: n = 7) was ventilated with PCV = 15 cm H(2)O for three consecutive 20-min periods (T1, T2, T3). In Group B (high PCV/normocapnia; n = 7), PCV was given at 20 (T1), 25 (T2), and 30 (T3) cm H(2)O. The targeted PCO(2) was 40 mm Hg in Groups A and B. Group C (high PCV/hypercapnia; n = 7) was ventilated in the same way as Group B, but the targeted PCO(2) was approximately equal to 70 to 100 mm Hg. The changes (from Baseline to T3) in weight gain (Delta WG: g) and in the ultrafiltration coefficient (Delta K(f) = gr/min/ cm H(2)O/100g) and the protein and hemoglobin concentrations in bronchoalveolar lavage fluid (BALF) were used to assess injury. Group B experienced a significantly greater Delta WG (14.85 +/- 5.49 [mean +/- SEM] g) and Delta K(f) (1.40 +/- 0.49 g/min/cm H(2)O/100 g) than did either Group A (Delta WG = 0.70 +/- 0.43; Delta K(f) = 0.01 +/- 0.03) or Group C (Delta WG = 5.27 +/- 2.03 g; Delta K(f) = 0.25 +/- 0.12 g/min/cm H(2)O/ 100 g). BALF protein and hemoglobin concentrations (g/L) were higher in Group B (11.98 +/- 3.78 g/L and 1.82 +/- 0.40 g/L, respectively) than in Group A (2.92 +/- 0.75 g/L and 0.38 +/- 0.15 g/L) or Group C (5.71 +/- 1.88 g/L and 1.19 +/- 0.32 g/L). We conclude that respiratory acidosis decreases the severity of VILI in this model.

Estudio de los mecanismos terapéuticos en la inducción de tolerancia immunológica en un modelo animal de esclerosis múltiple

En una serie de estudios previos demostramos que la infusión de células de médula ósea (MO) modificadas genéticamente para la expresión del autoantígeno MOG40-55 en ausencia de mieloablación inducía tolerancia antígenoespecífica en un modelo murino de esclerosis múltiple. También observamos que este efecto terapéutico no requería injerto hematopoyético. Nos propusimos estudiar si el efecto tolerogénico está inducido por una subpoblación de células generadas durante la transducción de la MO y el papel de las células T reguladoras en la inducción de la tolerancia. Las células de MO fueron cultivadas y transducidas usando medio complementado con 20% FCS y medios condicionados como fuente de stem cell factor (SCF) e IL-3 murinos. Las diferentes poblaciones celulares se separaron por citometría de flujo y se analizó la capacidad supresora de las poblaciones candidatas. Por otro lado se analizó la presencia de células T reguladoras en bazo y SNC de los ratones recuperados después de la infusión de células de MO transducidas. A los cinco días de cultivo, la mayoría de células presentaban fenotipo mieloide (Mac-1+Gr-1low/-:31,9+-10,2%; Mac-1+Gr-1high:26,0+-3,3%). Ambos fenotipos se corresponden con dos subpoblaciones de células mieloides supresoras (MDSC, tipo monocí¬tico y granulocítico respectivamente) descritas recientemente. Se estudió la capacidad de ambas poblaciones para suprimir la respuesta proliferativa específica de esplenocitos frente a MOG40-55 in vitro, observando una mayor capacidad de supresión de las MDSC monocíticas, que se correspondí¬a con niveles significativamente superiores de actividad de las enzimas arginasa-1 y sintasa de óxido nítrico (ambos mecanismos supresores característicos de las MDSC). A los 7 días del tratamiento no se observaron diferencias significativas en el porcentaje de células T reguladoras (Treg y Tr1) entre el grupo tratado (liM) y los grupos de control.

Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality.

Genomes of eusocial insects code for dramatic examples of phenotypic plasticity and social organization. We compared the genomes of seven ants, the honeybee, and various solitary insects to examine whether eusocial lineages share distinct features of genomic organization. Each ant lineage contains ∼4000 novel genes, but only 64 of these genes are conserved among all seven ants. Many gene families have been expanded in ants, notably those involved in chemical communication (e.g., desaturases and odorant receptors). Alignment of the ant genomes revealed reduced purifying selection compared with Drosophila without significantly reduced synteny. Correspondingly, ant genomes exhibit dramatic divergence of noncoding regulatory elements; however, extant conserved regions are enriched for novel noncoding RNAs and transcription factor-binding sites. Comparison of orthologous gene promoters between eusocial and solitary species revealed significant regulatory evolution in both cis (e.g., Creb) and trans (e.g., fork head) for nearly 2000 genes, many of which exhibit phenotypic plasticity. Our results emphasize that genomic changes can occur remarkably fast in ants, because two recently diverged leaf-cutter ant species exhibit faster accumulation of species-specific genes and greater divergence in regulatory elements compared with other ants or Drosophila. Thus, while the "socio-genomes" of ants and the honeybee are broadly characterized by a pervasive pattern of divergence in gene composition and regulation, they preserve lineage-specific regulatory features linked to eusociality. We propose that changes in gene regulation played a key role in the origins of insect eusociality, whereas changes in gene composition were more relevant for lineage-specific eusocial adaptations.

Marbofloxacin achieves high concentration in pig tonsils according to a dose dependent fashion

The penetration of marbofloxacin into tonsils was assessed in fattening pigs. Two different dosages were used to treat the animals: 2 mg/kg b.w. every 24 hours during 3 days (P1 group) and 4 mg/kg b.w. every 48 hours two times (P2 group. A ratio between the mean tonsillar concentration of marbofloxacin for both doses 24 hours after the last administration (0.5 and 0.7 µgr/mL) and its MIC90 for APP (0.03 µgr/mL) was calculated. These Ratio values were 16.6 and 23.3 for P1 and P2 group.

Sensitivity of Leishmania spp. to Glibenclamide and 4-Aminopiridine: A Tool for the Study of Drug Resistance Development

We have demonstrated that Leishmania spp. grown as promastigotes, are sensitive to the K+ channel inhibitors 4-aminopyridine and glibenclamide. Their host cells, the macrophages, are not affected by similar concentrations of the drugs. We have also initiated the molecular characterization of the mechanisms involved in the development of drug resistance to glibenclamide by the parasite. Therefore, we have selected experimentally and begun to characterize the Venezuelan Leishmania (Leishmania) strain, NR resistant to glibenclamide [NR(Gr)]. The analysis of genomic DNA evidenced the existence of a fragment which apparently is amplified in NR(Gr). The fragment recognized by the pgpA probe, related to the Leishmania P-glycoprotein family and which was originally isolated from L. tarentolae, showed a size polymorfism between the sensitive and the resistant strain. These results suggest that the development of resistance to glibenclamide in the strain NR(Gr) might be associated with the amplification of the ltpgpA or related gene(s)

Novel H3K4me3 marks are enriched at human- and chimpanzee-specific cytogenetic structures.

Human and chimpanzee genomes are 98.8% identical within comparable sequences. However, they differ structurally in nine pericentric inversions, one fusion that originated human chromosome 2, and content and localization of heterochromatin and lineage-specific segmental duplications. The possible functional consequences of these cytogenetic and structural differences are not fully understood and their possible involvement in speciation remains unclear. We show that subtelomeric regions-regions that have a species-specific organization, are more divergent in sequence, and are enriched in genes and recombination hotspots-are significantly enriched for species-specific histone modifications that decorate transcription start sites in different tissues in both human and chimpanzee. The human lineage-specific chromosome 2 fusion point and ancestral centromere locus as well as chromosome 1 and 18 pericentric inversion breakpoints showed enrichment of human-specific H3K4me3 peaks in the prefrontal cortex. Our results reveal an association between plastic regions and potential novel regulatory elements.

NLRP3 Suppresses NK Cell-Mediated Responses to Carcinogen-Induced Tumors and Metastases.

The NLRP3 inflammasome acts as a danger signal sensor that triggers and coordinates the inflammatory response upon infectious insults or tissue injury and damage. However, the role of the NLRP3 inflammasome in natural killer (NK) cell-mediated control of tumor immunity is poorly understood. Here, we show in a model of chemical-induced carcinogenesis and a series of experimental and spontaneous metastases models that mice lacking NLRP3 display significantly reduced tumor burden than control wild-type (WT) mice. The suppression of spontaneous and experimental tumor metastases and methylcholanthrene (MCA)-induced sarcomas in mice deficient for NLRP3 was NK cell and IFN-γ-dependent. Focusing on the amenable B16F10 experimental lung metastases model, we determined that expression of NLRP3 in bone marrow-derived cells was necessary for optimal tumor metastasis. Tumor-driven expansion of CD11b(+)Gr-1(intermediate) (Gr-1(int)) myeloid cells within the lung tumor microenvironment of NLRP3(-/-) mice was coincident with increased lung infiltrating activated NK cells and an enhanced antimetastatic response. The CD11b(+)Gr-1(int) myeloid cells displayed a unique cell surface phenotype and were characterized by their elevated production of CCL5 and CXCL9 chemokines. Adoptive transfer of this population into WT mice enhanced NK cell numbers in, and suppression of, B16F10 lung metastases. Together, these data suggested that NLRP3 is an important suppressor of NK cell-mediated control of carcinogenesis and metastases and identify CD11b(+)Gr-1(int) myeloid cells that promote NK cell antimetastatic function. Cancer Res; 72(22); 5721-32. ©2012 AACR.

Age-dependent gain of alternative splice forms and biased duplication explain the relation between splicing and duplication.

We analyze here the relation between alternative splicing and gene duplication in light of recent genomic data, with a focus on the human genome. We show that the previously reported negative correlation between level of alternative splicing and family size no longer holds true. We clarify this pattern and show that it is sufficiently explained by two factors. First, genes progressively gain new splice variants with time. The gain is consistent with a selectively relaxed regime, until purifying selection slows it down as aging genes accumulate a large number of variants. Second, we show that duplication does not lead to a loss of splice forms, but rather that genes with low levels of alternative splicing tend to duplicate more frequently. This leads us to reconsider the role of alternative splicing in duplicate retention.

Promoter architecture of mouse olfactory receptor genes.

Odorous chemicals are detected by the mouse main olfactory epithelium (MOE) by about 1100 types of olfactory receptors (OR) expressed by olfactory sensory neurons (OSNs). Each mature OSN is thought to express only one allele of a single OR gene. Major impediments to understand the transcriptional control of OR gene expression are the lack of a proper characterization of OR transcription start sites (TSSs) and promoters, and of regulatory transcripts at OR loci. We have applied the nanoCAGE technology to profile the transcriptome and the active promoters in the MOE. nanoCAGE analysis revealed the map and architecture of promoters for 87.5% of the mouse OR genes, as well as the expression of many novel noncoding RNAs including antisense transcripts. We identified candidate transcription factors for OR gene expression and among them confirmed by chromatin immunoprecipitation the binding of TBP, EBF1 (OLF1), and MEF2A to OR promoters. Finally, we showed that a short genomic fragment flanking the major TSS of the OR gene Olfr160 (M72) can drive OSN-specific expression in transgenic mice.