Oscillating Taylor bubble during the emptying of a partially filled water bottle.

The oscillatory behavior observed during the emptying of a vertical cylinder partially filled with water has been studied for large neck-to-bottle diameter ratios, d^{*}. For large apertures (d^{*}>0.8), a Taylor bubble invades the cylinder from the bottom, and its rising speed exhibits periodic oscillations coupled to periodic motions of the free surface limiting the top air buffer initially present in the bottle.

Critical COPD respiratory illness is linked to increased transcriptomic activity of neutrophil proteases genes.

Background: Gene expression profiling (GEP) in cells obtained from peripheral blood has shown that this is a very useful approach for biomarker discovery and for studying molecular pathogenesis of prevalent diseases. While there is limited literature available on gene expression markers associated with Chronic Obstructive Pulmonary Disease (COPD), the transcriptomic picture associated with critical respiratory illness in this disease is not known at the present moment.

Findings: By using Agilent microarray chips, we have profiled gene expression signatures in the whole blood of 28 COPD patients hospitalized with different degrees of respiratory compromise.

Viral infection is associated with an increased proinflammatory response in chronic obstructive pulmonary disease.

The development of new diagnostic methods based on molecular biology has led to evidence of the important role of respiratory viruses in chronic obstructive pulmonary disease (COPD) exacerbations. Cytokines and chemokines are recognized as key actors in the pathogenesis of COPD. The objective of this study was to evaluate the association between viral infection and host cytokine responses in 57 COPD patients hospitalized with an acute exacerbation.

Interaction and coalescence of large bubbles rising in a thin gap.

We present accurate measurements of the relative motion and deformation of two large bubbles released consecutively in a quiescent liquid confined in a thin-gap cell. Although the second injected bubble was smaller, we observed that, in all cases, it accelerated and caught up with the leading bubble. This acceleration is related to the wake of the leading bubble, which also induces significant changes in the width and curvature of the trailing bubble.

Host response cytokine signatures in viral and nonviral acute exacerbations of chronic obstructive pulmonary disease.

Viruses are strongly associated with acute exacerbations of chronic obstructive pulmonary disease (AECOPD). Interferon-inducible protein-10 has been recently described as a biomarker of human rhinovirus infection, but there are no reports on the role of other immune mediators in AECOPD of viral origin. As an attempt to evaluate the differences in the systemic immune mediators profiles between AECOPD patients with presence/absence of viral infection, we measured 27 cytokines, chemokines, and cellular growth factors in the plasma of 40 patients with AECOPD needing of hospitalization by using a Luminex-based assay.

[Comparative study between oral azathioprine and intravenous cyclophosphamide pulses in the treatment of idiopathic pulmonary fibrosis].

Introduction: The purpose of the study was to establish the efficacy of treatment with intravenous cyclophosphamide pulses and oral corticoids in idiopathic pulmonary fibrosis, compared with the standard treatment with corticoids and azathioprine.

Patients And Method: A prospective, non-controlled study with 2 parallel groups. One group received prednisone plus oral azathioprine for 24 months (AZA group).

Synthesis and anti-HIV-1 integrase activity of modified dinucleotides.

The synthesis of a series of thirty-eight new modified dinucleotides and dinucleotide conjugate analogues of d-(5')ApC(3') is described. The inhibitory activity of these compounds toward HIV-1 integrase was examined in enzymatic assays using the natural dinucleotide as a reference. Among the compounds, a perylene-dinucleotide conjugate has shown a two micromolar anti-integrase activity due to the presence of both the intercalator and the dinucleotide.

Triplex-forming oligonucleotide-orthophenanthroline conjugates for efficient targeted genome modification.

The inefficiency of gene modification by homologous recombination can be overcome by the introduction of a double-strand break (DSB) in the target. Engineering the endonucleases needed, however, remains a challenging task that limits widespread application of nuclease-driven gene modification. We report here that conjugates of orthophenanthroline (OP), a DNA cleaving molecule, and triplex-forming oligonucleotides (TFOs), known to bind specific DNA sequences, are synthetic nucleases efficient at stimulating targeted genome modification.

Wake attenuation in large Reynolds number dispersed two-phase flows.

The dynamics of high Reynolds number-dispersed two-phase flow strongly depends on the wakes generated behind the moving bodies that constitute the dispersed phase. The length of these wakes is considerably reduced compared with those developing behind isolated bodies. In this paper, this wake attenuation is studied from several complementary experimental investigations with the aim of determining how it depends on the body Reynolds number and the volume fraction alpha.

Detection of terminal mismatches on DNA duplexes in homogeneous assays or with immobilized probes.

We recently reported the design of new fluorescent oligo-2'-deoxyribonucleotides (FODNs) for the detection of terminal mismatches on DNA duplexes in homogeneous assays. We now report the validation of this method in homogeneous assays with other sequences and the feasibility of the detection of terminal mismatches with immobilized FODNs. In all cases studied, the mismatched duplexes were more fluorescent than the perfect ones and results confirmed that the discrimination factor is sequence-dependent.

Detection of terminal mismatches on DNA duplexes with fluorescent oligonucleotides.

This paper describes the design of terminal-mismatch discriminating fluorescent oligonucleotides (TMDFOs). The method is based on the use of sets of oligo-2'-deoxyribonucleotide probes linked via their 5'-ends, and varying-sized flexible polymethylene chains, to thiazole orange, with the linker being attached to the benzothiazole moiety. The sequence of each set of labelled probes was identical and complementary to the sequence to be analyzed on the single-stranded nucleic acid target except at the interrogation position, located at the 5'-end of the probes in a position adjacent to the attachment site of the label, where each of the four nucleic bases were incorporated.

Intercalator conjugates of pyrimidine locked nucleic acid-modified triplex-forming oligonucleotides: improving DNA binding properties and reaching cellular activities.

Triplex-forming oligonucleotides (TFOs) are powerful tools to interfere sequence-specifically with DNA-associated biological functions. (A/T,G)-containing TFOs are more commonly used in cells than (T,C)-containing TFOs, especially C-rich sequences; indeed the low intracellular stability of the non-covalent pyrimidine triplexes make the latter less active. In this work we studied the possibility to enhance DNA binding of (T,C)-containing TFOs, aiming to reach cellular activities; to this end, we used locked nucleic acid-modified TFOs (TFO/LNAs) in association with 5'-conjugation of an intercalating agent, an acridine derivative.

Oligo-2'-deoxyribonucleotides containing uracil modified at the 5-position with linkers ending with guanidinium groups.

We report here the synthesis and binding studies of oligo-2'-deoxyribonucleotides (ODNs) containing 2'-deoxyuridines, modified at the 5-position by linkers ending with either one or two guanidinium groups. Comparison was made with ODNs containing 2'-deoxyuridines modified at the 5-position with linkers ending with either two or one amino groups. One or two modified 2'-deoxyuridines were incorporated into pyrimidine strands, and their influence on the stability of duplex (with both DNA and RNA targets) and triplex structures was studied.

Synthesis and binding properties of oligo-2'-deoxyribonucleotides conjugated with triple-helix-specific intercalators: benzo[e] and benzo[g] pyridoindoles.

DNA binding compounds, such as benzo[e] (BePI) and benzo[g] pyridoindole (BgPI) derivatives, exhibit preferential stabilization of triple helices. We report here the synthesis of a series of pyrimidine triple-helix-forming oligo-2'-deoxyribonucleotides conjugated with these molecules. BePI was coupled to the 5-position of 2'-deoxyuridine via two linkers of different sizes attached to its 11-position and placed at either the 5'-end, inside the sequence, or at both the 5'-end and the internal positions using periodate oxidation of a diol-containing oligonucleotide followed by reductive coupling with amino-linked BePI.

Excimer laser photorefractive keratectomy for high myopia.

One hundred and thirty-three eyes of 103 patients had photorefractive keratectomy with a slit scan mode excimer laser for myopia ranging from -6.00 to -22.00 diopters (D).

Monoclonal antibodies targeted to alpha-oligonucleotides. Characterisation and application in nucleic acid detection.

The aim of the present study was to test the antigenicity of alpha-deoxyribonucleotides in order to develop a new tool for the detection of nucleic acid sequences for use in diagnostic applications. We describe four monoclonal antibodies (Mabs) which recognize alpha-deoxyribonucleotides. Two were raised against a poly(alpha-dT) sequence and specifically recognized the alpha-dT nucleotide.

Crystallization and preliminary X-ray analysis of the catalytic domain of endoglucanase from Clostridium cellulolyticum.

The catalytic domain of an endoglucanase belonging to family A (CelCCA) from an anaerobic bacterium (Clostridium cellulolyticum) has been crystallized in a form suitable for X-ray diffraction analysis. The crystals have been grown in the presence of polyethylene glycol 4000 using the vapour diffusion technique. The crystals, which diffract to 2.

Crystallization and preliminary crystallographic study of an octa-heme cytochrome c3 from Desulfovibrio desulfuricans Norway.

An octa-heme cytochrome c3, isolated as a dimeric molecule of about 30 kDa from the anaerobic bacteria Desulfovibro desulfuricans Norway, has been crystallized in a form suitable for atomic resolution X-ray structural investigations. The crystals are trigonal, space group P3(1)21 (or its enantiomorph P3(2)21), with cell dimensions: a = b = 72.9 A c = 62.

Inhibition of translation initiation by antisense oligonucleotides via an RNase-H independent mechanism.

We have used alpha-oligomers as antisense oligonucleotides complementary to three different sequences of the rabbit beta-globin mRNA: a region adjacent to the cap site, a region spanning the AUG initiation codon or a sequence in the coding region. These alpha-oligonucleotides were synthesized either with a free 5' OH group or linked to an acridine derivative. The effect of these oligonucleotides on mRNA translation was investigated in cell-free extracts and in Xenopus oocytes.

Sequence-specific intercalating agents: intercalation at specific sequences on duplex DNA via major groove recognition by oligonucleotide-intercalator conjugates.

An acridine derivative was covalently linked to the 5' end of a homopyrimidine oligonucleotide. Specific binding to a homopurine-homopyrimidine sequence of duplex DNA was demonstrated by spectroscopic studies (absorption and fluorescence) and by "footprinting" experiments with a copper phenanthroline chelate used as an artificial nuclease. A hypochromism and a red shift of the acridine absorption were observed.

2D-NMR studies of the unnatural duplex alpha-d(TCTAAAC)-beta-d(AGATTTG).

The unnatural oligonucleotide alpha-d(TCTAAAC) was synthesized and was found more resistant towards endonucleases than its beta-analog. 2D-NMR experiments allowed the assignment of all non-exchangeable aromatic and sugar protons except for the overlapping 5' -5" resonances, as well as the exchangeable imino protons of the parallel hybrid duplex alpha-d (TCTAAAC)-beta-d(AGATTTG). NMR studies show that the strength of the association between the alpha-strand and the beta parallel strand is equivalent to that between their anti-parallel complementary beta-analogs beta-d(CAAATCT) and beta-d(AGATTTG).

Oligo(alpha-deoxynucleotide)s covalently linked to intercalating agents: differential binding to ribo- and deoxyribopolynucleotides and stability towards nuclease digestion.

An octathymidylate was synthesized with the alpha anomer of thymidine instead of the naturally occurring beta anomer. This oligonucleotide binds to complementary sequences containing beta-nucleosides. Binding to ribose-containing oligomers and polymers is much stronger than binding to deoxyribose-containing analogs.